| 2006-04-03 | vs ATL | 1 | L 10-11 | 0-1 | 4 | 56,000 | Derek Lowe | Tim Hudson | Oscar Villarreal | Derek Lowe | Chris Reitsma | 10 | 11 | -1 |
| 2006-04-04 | vs ATL | 2 | W 5-4 | 1-1 | 3 | 36,249 | Brad Penny | John Smoltz | Brad Penny | John Smoltz | Danys Baez | 15 | 15 | 0 |
| 2006-04-05 | vs ATL | 3 | L 8-9 | 1-2 | 5 | 35,292 | Odalis Perez | Horacio Ramirez | Oscar Villarreal | Franquelis Osoria | Chris Reitsma | 23 | 24 | -1 |
| 2006-04-07 | @ PHI | 4 | W 5-3 | 2-2 | 3 | 25,518 | Brett Tomko | Gavin Floyd | Brett Tomko | Gavin Floyd | Danys Baez | 28 | 27 | 1 |
| 2006-04-09 | @ PHI | 5 | L 3-6 | 3-3 | 4 | 0 | Derek Lowe | Ryan Madson | Tom Gordon | Tim Hamulack | | 31 | 33 | -2 |
| 2006-04-09 | @ PHI | 6 | W 6-2 | 3-3 | 4 | 38,056 | Brad Penny | Jon Lieber | Brad Penny | Jon Lieber | | 37 | 35 | 2 |
| 2006-04-10 | @ PIT | 7 | W 8-3 | 4-3 | 3 | 39,129 | Odalis Perez | Zach Duke | Odalis Perez | Zach Duke | | 45 | 38 | 7 |
| 2006-04-11 | @ PIT | 8 | L 6-7 | 4-4 | 3 | 17,240 | Jae Weong Seo | Ian Snell | Salomon Torres | Lance Carter | Mike Gonzalez | 51 | 45 | 6 |
| 2006-04-12 | @ PIT | 9 | L 5-9 | 4-5 | 4 | 13,237 | Brett Tomko | Paul Maholm | Salomon Torres | Hong-Chih Kuo | | 56 | 54 | 2 |
| 2006-04-13 | @ PIT | 10 | W 13-5 | 5-5 | 3 | 18,134 | Derek Lowe | Oliver Perez | Derek Lowe | Oliver Perez | | 69 | 59 | 10 |
| 2006-04-14 | vs SFN | 11 | L 1-2 | 5-6 | 4 | 45,940 | Brad Penny | Jamey Wright | Jamey Wright | Hong-Chih Kuo | Tim Worrell | 70 | 61 | 9 |
| 2006-04-15 | vs SFN | 12 | W 3-1 | 6-6 | 3 | 55,132 | Odalis Perez | Jason Schmidt | Odalis Perez | Jason Schmidt | Danys Baez | 73 | 62 | 11 |
| 2006-04-16 | vs SFN | 13 | L 0-2 | 6-7 | 3 | 47,024 | Jae Weong Seo | Brad Hennessey | Brad Hennessey | Jae Weong Seo | Tim Worrell | 73 | 64 | 9 |
| 2006-04-17 | vs CHN | 14 | L 1-4 | 6-8 | 3 | 33,511 | Brett Tomko | Greg Maddux | Greg Maddux | Brett Tomko | Ryan Dempster | 74 | 68 | 6 |
| 2006-04-18 | vs CHN | 15 | W 2-1 | 7-8 | 3 | 37,342 | Derek Lowe | Carlos Zambrano | Takashi Saito | Will Ohman | | 76 | 69 | 7 |
| 2006-04-19 | vs CHN | 16 | L 4-5 | 7-9 | 4 | 41,288 | Brad Penny | Sean Marshall | Scott Williamson | Danys Baez | Ryan Dempster | 80 | 74 | 6 |
| 2006-04-21 | vs ARI | 17 | W 6-3 | 8-9 | 3 | 44,294 | Odalis Perez | Orlando Hernandez | Odalis Perez | Orlando Hernandez | Danys Baez | 86 | 77 | 9 |
| 2006-04-22 | vs ARI | 18 | L 4-5 | 8-10 | 4 | 51,878 | Jae Weong Seo | Miguel Batista | Miguel Batista | Jae Weong Seo | Jose Valverde | 90 | 82 | 8 |
| 2006-04-23 | vs ARI | 19 | W 6-4 | 9-10 | 3 | 48,394 | Brett Tomko | Russ Ortiz | Brett Tomko | Russ Ortiz | Danys Baez | 96 | 86 | 10 |
| 2006-04-24 | @ HOU | 20 | W 6-2 | 10-10 | 3 | 28,382 | Derek Lowe | Andy Pettitte | Takashi Saito | Brad Lidge | Danys Baez | 102 | 88 | 14 |
| 2006-04-25 | @ HOU | 21 | L 3-4 | 10-11 | 4 | 30,451 | Brad Penny | Fernando Nieve | Ezequiel Astacio | Hong-Chih Kuo | | 105 | 92 | 13 |
| 2006-04-26 | @ HOU | 22 | L 5-8 | 10-12 | 4 | 32,874 | Odalis Perez | Wandy Rodriguez | Wandy Rodriguez | Odalis Perez | | 110 | 100 | 10 |
| 2006-04-28 | @ SDN | 23 | W 3-0 | 11-12 | 4 | 36,435 | Jae Weong Seo | Chris Young | Jae Weong Seo | Chris Young | Danys Baez | 113 | 100 | 13 |
| 2006-04-29 | @ SDN | 24 | W 4-2 | 12-12 | 3 | 44,337 | Brett Tomko | Clay Hensley | Brett Tomko | Clay Hensley | Danys Baez | 117 | 102 | 15 |
| 2006-04-30 | @ SDN | 25 | L 5-6 | 12-13 | 4 | 38,116 | Derek Lowe | Chan Ho Park | Scott Linebrink | Tim Hamulack | | 122 | 108 | 14 |
| 2006-05-01 | @ ARI | 26 | L 2-3 | 12-14 | 4 | 20,099 | Brad Penny | Claudio Vargas | Claudio Vargas | Brad Penny | Jose Valverde | 124 | 111 | 13 |
| 2006-05-02 | @ ARI | 27 | L 8-10 | 12-15 | 4 | 23,198 | Odalis Perez | Orlando Hernandez | Luis Vizcaino | Takashi Saito | Jose Valverde | 132 | 121 | 11 |
| 2006-05-03 | vs SDN | 28 | L 5-11 | 12-16 | 5 | 33,352 | Jae Weong Seo | Chris Young | Scott Cassidy | Franquelis Osoria | | 137 | 132 | 5 |
| 2006-05-04 | vs SDN | 29 | L 0-3 | 12-17 | 5 | 34,137 | Brett Tomko | Clay Hensley | Alan Embree | Takashi Saito | Trevor Hoffman | 137 | 135 | 2 |
| 2006-05-05 | vs MIL | 30 | W 4-3 | 13-17 | 5 | 47,731 | Derek Lowe | Chris Capuano | Danys Baez | Matt Wise | | 141 | 138 | 3 |
| 2006-05-06 | vs MIL | 31 | W 5-4 | 14-17 | 5 | 46,087 | Brad Penny | Ben Hendrickson | Danys Baez | Chris Demaria | | 146 | 142 | 4 |
| 2006-05-07 | vs MIL | 32 | W 10-2 | 15-17 | 4 | 53,532 | Aaron Sele | David Bush | Aaron Sele | David Bush | | 156 | 144 | 12 |
| 2006-05-09 | vs HOU | 33 | W 12-7 | 16-17 | 4 | 55,992 | Jae Weong Seo | Andy Pettitte | Takashi Saito | Dan Wheeler | | 168 | 151 | 17 |
| 2006-05-10 | vs HOU | 34 | W 9-6 | 17-17 | 4 | 33,595 | Brett Tomko | Taylor Buchholz | Brett Tomko | Taylor Buchholz | | 177 | 157 | 20 |
| 2006-05-11 | vs HOU | 35 | L 2-4 | 17-18 | 4 | 37,133 | Derek Lowe | Wandy Rodriguez | Wandy Rodriguez | Derek Lowe | Dan Wheeler | 179 | 161 | 18 |
| 2006-05-12 | @ SFN | 36 | W 6-1 | 18-18 | 4 | 42,885 | Brad Penny | Matt Morris | Brad Penny | Matt Morris | | 185 | 162 | 23 |
| 2006-05-13 | @ SFN | 37 | L 5-6 | 18-19 | 4 | 42,864 | Aaron Sele | Noah Lowry | Armando Benitez | Danys Baez | | 190 | 168 | 22 |
| 2006-05-14 | @ SFN | 38 | W 6-3 | 19-19 | 4 | 42,984 | Jae Weong Seo | Jason Schmidt | Odalis Perez | Steve Kline | Joe Beimel | 196 | 171 | 25 |
| 2006-05-15 | @ COL | 39 | W 5-4 | 20-19 | 4 | 20,208 | Brett Tomko | Josh Fogg | Brett Tomko | Ramon Ramirez | Takashi Saito | 201 | 175 | 26 |
| 2006-05-16 | @ COL | 40 | L 1-5 | 20-20 | 4 | 23,192 | Derek Lowe | Byung-Hyun Kim | Byung-Hyun Kim | Derek Lowe | | 202 | 180 | 22 |
| 2006-05-17 | @ COL | 41 | W 3-2 | 21-20 | 4 | 30,296 | Brad Penny | Jason Jennings | Brad Penny | Jason Jennings | Danys Baez | 205 | 182 | 23 |
| 2006-05-19 | vs ANA | 42 | W 16-3 | 22-20 | 4 | 55,655 | Aaron Sele | Jeff Weaver | Aaron Sele | Jeff Weaver | | 221 | 185 | 36 |
| 2006-05-20 | vs ANA | 43 | W 8-4 | 23-20 | 3 | 55,587 | Brett Tomko | Kevin Gregg | Joe Beimel | Scot Shields | | 229 | 189 | 40 |
| 2006-05-21 | vs ANA | 44 | W 7-0 | 24-20 | 3 | 55,662 | Derek Lowe | Ervin Santana | Derek Lowe | Ervin Santana | | 236 | 189 | 47 |
| 2006-05-22 | vs COL | 45 | W 6-1 | 25-20 | 3 | 33,652 | Jae Weong Seo | Byung-Hyun Kim | Jae Weong Seo | Byung-Hyun Kim | | 242 | 190 | 52 |
| 2006-05-23 | vs COL | 46 | W 8-1 | 26-20 | 2 | 40,228 | Brad Penny | Jason Jennings | Brad Penny | Jason Jennings | | 250 | 191 | 59 |
| 2006-05-24 | vs COL | 47 | W 7-1 | 27-20 | 2 | 39,299 | Aaron Sele | Aaron Cook | Aaron Sele | Aaron Cook | | 257 | 192 | 65 |
| 2006-05-26 | @ WAS | 48 | L 4-10 | 27-21 | 2 | 22,712 | Brett Tomko | Livan Hernandez | Livan Hernandez | Brett Tomko | | 261 | 202 | 59 |
| 2006-05-27 | @ WAS | 49 | W 3-1 | 28-21 | 2 | 26,867 | Derek Lowe | Shawn Hill | Derek Lowe | Mike Stanton | Takashi Saito | 264 | 203 | 61 |
| 2006-05-28 | @ WAS | 50 | L 4-10 | 28-22 | 2 | 30,348 | Jae Weong Seo | Ramon Ortiz | Ramon Ortiz | Jae Weong Seo | | 268 | 213 | 55 |
| 2006-05-29 | @ ATL | 51 | W 12-5 | 29-22 | 2 | 41,825 | Brad Penny | John Thomson | Joe Beimel | John Thomson | | 280 | 218 | 62 |
| 2006-05-30 | @ ATL | 52 | W 8-3 | 30-22 | 2 | 29,517 | Aaron Sele | Jorge Sosa | Danys Baez | Mike Remlinger | | 288 | 221 | 67 |
| 2006-05-31 | @ ATL | 53 | L 3-9 | 30-23 | 2 | 28,880 | Brett Tomko | Tim Hudson | Tim Hudson | Brett Tomko | | 291 | 230 | 61 |
| 2006-06-01 | vs PHI | 54 | W 7-2 | 31-23 | 2 | 38,643 | Derek Lowe | Gavin Floyd | Derek Lowe | Gavin Floyd | | 298 | 232 | 66 |
| 2006-06-02 | vs PHI | 55 | L 6-8 | 31-24 | 2 | 55,142 | Jae Weong Seo | Ryan Madson | Geoff Geary | Danys Baez | Tom Gordon | 304 | 240 | 64 |
| 2006-06-03 | vs PHI | 56 | W 8-2 | 32-24 | 2 | 46,561 | Brad Penny | Eude Brito | Brad Penny | Eude Brito | | 312 | 242 | 70 |
| 2006-06-04 | vs PHI | 57 | L 4-6 | 32-25 | 2 | 48,270 | Aaron Sele | Brett Myers | Geoff Geary | Joe Beimel | Tom Gordon | 316 | 248 | 68 |
| 2006-06-05 | vs NYN | 58 | L 1-4 | 32-26 | 2 | 34,420 | Brett Tomko | Alay Soler | Alay Soler | Brett Tomko | Chad Bradford | 317 | 252 | 65 |
| 2006-06-06 | vs NYN | 59 | W 8-5 | 33-26 | 2 | 46,347 | Derek Lowe | Pedro Martinez | Derek Lowe | Pedro Martinez | Eric Gagne | 325 | 257 | 68 |
| 2006-06-07 | vs NYN | 60 | L 7-9 | 33-27 | 2 | 44,230 | Odalis Perez | Tom Glavine | Tom Glavine | Odalis Perez | Billy Wagner | 332 | 266 | 66 |
| 2006-06-09 | @ COL | 61 | W 3-0 | 34-27 | 2 | 30,455 | Brad Penny | Byung-Hyun Kim | Brad Penny | Byung-Hyun Kim | Takashi Saito | 335 | 266 | 69 |
| 2006-06-10 | @ COL | 62 | L 9-12 | 34-28 | 2 | 35,557 | Brett Tomko | Jason Jennings | Jason Jennings | Brett Tomko | Brian Fuentes | 344 | 278 | 66 |
| 2006-06-11 | @ COL | 63 | W 6-5 | 35-28 | 1 | 29,221 | Derek Lowe | Aaron Cook | Danys Baez | Brian Fuentes | Takashi Saito | 350 | 283 | 67 |
| 2006-06-13 | @ SDN | 64 | L 1-9 | 35-29 | 2 | 30,371 | Aaron Sele | Chan Ho Park | Chan Ho Park | Aaron Sele | | 351 | 292 | 59 |
| 2006-06-14 | @ SDN | 65 | L 3-5 | 35-30 | 2 | 30,011 | Brad Penny | Mike Thompson | Scott Linebrink | Hong-Chih Kuo | Trevor Hoffman | 354 | 297 | 57 |
| 2006-06-15 | @ SDN | 66 | W 7-3 | 36-30 | 1 | 33,382 | Chad Billingsley | Chris Young | Jonathan Broxton | Brian Sikorski | | 361 | 300 | 61 |
| 2006-06-16 | @ OAK | 67 | L 3-7 | 36-31 | 1 | 30,161 | Brett Tomko | Barry Zito | Barry Zito | Brett Tomko | | 364 | 307 | 57 |
| 2006-06-17 | @ OAK | 68 | L 4-5 | 36-32 | 1 | 35,077 | Derek Lowe | Kirk Saarloos | Steve Karsay | Jae Weong Seo | | 368 | 312 | 56 |
| 2006-06-18 | @ OAK | 69 | L 2-5 | 36-33 | 1 | 35,077 | Aaron Sele | Joe Blanton | Joe Blanton | Aaron Sele | Huston Street | 370 | 317 | 53 |
| 2006-06-20 | vs SEA | 70 | L 4-9 | 36-34 | 2 | 43,949 | Brad Penny | Joel Pineiro | Joel Pineiro | Brad Penny | Rafael Soriano | 374 | 326 | 48 |
| 2006-06-21 | vs SEA | 71 | L 5-8 | 36-35 | 2 | 40,419 | Chad Billingsley | Jarrod Washburn | Julio Mateo | Danys Baez | J.J. Putz | 379 | 334 | 45 |
| 2006-06-22 | vs SEA | 72 | W 4-2 | 37-35 | 2 | 46,207 | Derek Lowe | Felix Hernandez | Derek Lowe | Felix Hernandez | | 383 | 336 | 47 |
| 2006-06-23 | vs PIT | 73 | W 10-4 | 38-35 | 2 | 55,823 | Brett Tomko | Oliver Perez | Brett Tomko | Oliver Perez | | 393 | 340 | 53 |
| 2006-06-24 | vs PIT | 74 | W 7-0 | 39-35 | 1 | 47,785 | Aaron Sele | Zach Duke | Aaron Sele | Zach Duke | | 400 | 340 | 60 |
| 2006-06-25 | vs PIT | 75 | W 7-4 | 40-35 | 1 | 55,545 | Brad Penny | Kip Wells | Brad Penny | Kip Wells | Takashi Saito | 407 | 344 | 63 |
| 2006-06-26 | @ MIN | 76 | L 2-8 | 40-36 | 1 | 22,528 | Chad Billingsley | Carlos Silva | Carlos Silva | Chad Billingsley | | 409 | 352 | 57 |
| 2006-06-27 | @ MIN | 77 | L 2-9 | 40-37 | 2 | 30,681 | Derek Lowe | Francisco Liriano | Francisco Liriano | Derek Lowe | | 411 | 361 | 50 |
| 2006-06-28 | @ MIN | 78 | L 3-6 | 40-38 | 3 | 34,157 | Odalis Perez | Johan Santana | Johan Santana | Odalis Perez | Joe Nathan | 414 | 367 | 47 |
| 2006-06-30 | @ ANA | 79 | W 6-1 | 41-38 | 3 | 44,233 | Brad Penny | Bartolo Colon | Brad Penny | Bartolo Colon | | 420 | 368 | 52 |
| 2006-07-01 | @ ANA | 80 | L 2-9 | 41-39 | 3 | 43,891 | Mark Hendrickson | Kelvim Escobar | Kelvim Escobar | Mark Hendrickson | | 422 | 377 | 45 |
| 2006-07-02 | @ ANA | 81 | L 0-4 | 41-40 | 4 | 44,223 | Chad Billingsley | John Lackey | John Lackey | Chad Billingsley | | 422 | 381 | 41 |
| 2006-07-03 | vs ARI | 82 | W 10-4 | 42-40 | 4 | 47,698 | Derek Lowe | Juan Cruz | Derek Lowe | Juan Cruz | | 432 | 385 | 47 |
| 2006-07-04 | vs ARI | 83 | W 11-3 | 43-40 | 2 | 55,816 | Aaron Sele | Enrique Gonzalez | Aaron Sele | Enrique Gonzalez | | 443 | 388 | 55 |
| 2006-07-05 | vs ARI | 84 | W 5-4 | 44-40 | 2 | 38,505 | Brad Penny | Claudio Vargas | Brad Penny | Claudio Vargas | Takashi Saito | 448 | 392 | 56 |
| 2006-07-06 | vs SFN | 85 | L 4-5 | 44-41 | 3 | 42,515 | Mark Hendrickson | Matt Cain | Brad Hennessey | Mark Hendrickson | Armando Benitez | 452 | 397 | 55 |
| 2006-07-07 | vs SFN | 86 | W 9-7 | 45-41 | 2 | 53,991 | Chad Billingsley | Matt Morris | Danys Baez | Jeremy Accardo | Takashi Saito | 461 | 404 | 57 |
| 2006-07-08 | vs SFN | 87 | L 7-11 | 45-42 | 2 | 46,496 | Derek Lowe | Noah Lowry | Noah Lowry | Derek Lowe | Armando Benitez | 468 | 415 | 53 |
| 2006-07-09 | vs SFN | 88 | W 3-1 | 46-42 | 2 | 41,849 | Aaron Sele | Jason Schmidt | Aaron Sele | Jason Schmidt | Takashi Saito | 471 | 416 | 55 |
| 2006-07-13 | @ SLN | 89 | L 2-3 | 46-43 | 2 | 45,156 | Chad Billingsley | Jason Marquis | Braden Looper | Odalis Perez | | 473 | 419 | 54 |
| 2006-07-14 | @ SLN | 90 | L 0-5 | 46-44 | 2 | 45,704 | Derek Lowe | Chris Carpenter | Chris Carpenter | Derek Lowe | | 473 | 424 | 49 |
| 2006-07-15 | @ SLN | 91 | L 1-2 | 46-45 | 2 | 46,068 | Mark Hendrickson | Jeff Suppan | Braden Looper | Danys Baez | | 474 | 426 | 48 |
| 2006-07-16 | @ SLN | 92 | L 3-11 | 46-46 | 2 | 44,741 | Brad Penny | Anthony Reyes | Anthony Reyes | Brad Penny | | 477 | 437 | 40 |
| 2006-07-17 | @ ARI | 93 | L 3-8 | 46-47 | 3 | 23,518 | Aaron Sele | Enrique Gonzalez | Enrique Gonzalez | Aaron Sele | | 480 | 445 | 35 |
| 2006-07-18 | @ ARI | 94 | W 4-1 | 47-47 | 2 | 27,471 | Chad Billingsley | Juan Cruz | Chad Billingsley | Juan Cruz | | 484 | 446 | 38 |
| 2006-07-19 | @ ARI | 95 | L 0-8 | 47-48 | 4 | 23,583 | Derek Lowe | Miguel Batista | Miguel Batista | Derek Lowe | | 484 | 454 | 30 |
| 2006-07-20 | @ ARI | 96 | L 2-5 | 47-49 | 4 | 25,294 | Mark Hendrickson | Brandon Webb | Brandon Webb | Mark Hendrickson | Jorge Julio | 486 | 459 | 27 |
| 2006-07-21 | vs SLN | 97 | L 0-2 | 47-50 | 4 | 47,987 | Brad Penny | Jeff Suppan | Jeff Suppan | Brad Penny | Jason Isringhausen | 486 | 461 | 25 |
| 2006-07-22 | vs SLN | 98 | L 1-6 | 47-51 | 4 | 50,438 | Aaron Sele | Jeff Weaver | Jeff Weaver | Aaron Sele | | 487 | 467 | 20 |
| 2006-07-23 | vs SLN | 99 | L 1-6 | 47-52 | 4 | 43,650 | Chad Billingsley | Jason Marquis | Jason Marquis | Chad Billingsley | | 488 | 473 | 15 |
| 2006-07-24 | vs SDN | 100 | L 6-7 | 47-53 | 5 | 38,050 | Derek Lowe | Chris Young | Doug Brocail | Giovanni Carrara | Trevor Hoffman | 494 | 480 | 14 |
| 2006-07-25 | vs SDN | 101 | L 3-7 | 47-54 | 5 | 51,334 | Mark Hendrickson | Chan Ho Park | Chan Ho Park | Mark Hendrickson | | 497 | 487 | 10 |
| 2006-07-26 | vs SDN | 102 | L 3-10 | 47-55 | 5 | 44,181 | Brad Penny | Jake Peavy | Jake Peavy | Brad Penny | | 500 | 497 | 3 |
| 2006-07-28 | vs WAS | 103 | W 13-1 | 48-55 | 5 | 55,825 | Chad Billingsley | Tony Armas | Chad Billingsley | Tony Armas | | 513 | 498 | 15 |
| 2006-07-29 | vs WAS | 104 | W 7-5 | 49-55 | 5 | 41,540 | Derek Lowe | Mike O'Connor | Derek Lowe | Mike O'Connor | Jonathan Broxton | 520 | 503 | 17 |
| 2006-07-30 | vs WAS | 105 | W 4-3 | 50-55 | 5 | 43,346 | Mark Hendrickson | Ramon Ortiz | Jonathan Broxton | Jon Rauch | Takashi Saito | 524 | 506 | 18 |
| 2006-08-01 | @ CIN | 106 | W 10-4 | 51-55 | 4 | 25,127 | Aaron Sele | Bronson Arroyo | Aaron Sele | Bill Bray | | 534 | 510 | 24 |
| 2006-08-02 | @ CIN | 107 | W 5-3 | 52-55 | 4 | 22,110 | Brad Penny | Elizardo Ramirez | Brad Penny | Elizardo Ramirez | Takashi Saito | 539 | 513 | 26 |
| 2006-08-03 | @ CIN | 108 | W 3-0 | 53-55 | 3 | 26,053 | Greg Maddux | Eric Milton | Greg Maddux | Eric Milton | Takashi Saito | 542 | 513 | 29 |
| 2006-08-04 | @ FLO | 109 | W 6-2 | 54-55 | 3 | 15,416 | Derek Lowe | Anibal Sanchez | Derek Lowe | Anibal Sanchez | | 548 | 515 | 33 |
| 2006-08-05 | @ FLO | 110 | W 10-2 | 55-55 | 3 | 17,863 | Chad Billingsley | Josh Johnson | Chad Billingsley | Josh Johnson | | 558 | 517 | 41 |
| 2006-08-06 | @ FLO | 111 | W 7-3 | 56-55 | 3 | 14,182 | Mark Hendrickson | Scott Olsen | Mark Hendrickson | Scott Olsen | | 565 | 520 | 45 |
| 2006-08-07 | vs COL | 112 | W 7-2 | 57-55 | 2 | 44,593 | Brad Penny | Josh Fogg | Brad Penny | Josh Fogg | | 572 | 522 | 50 |
| 2006-08-08 | vs COL | 113 | W 4-2 | 58-55 | 2 | 50,210 | Greg Maddux | Byung-Hyun Kim | Brett Tomko | Byung-Hyun Kim | Takashi Saito | 576 | 524 | 52 |
| 2006-08-09 | vs COL | 114 | L 1-3 | 58-56 | 3 | 46,643 | Derek Lowe | Jeff Francis | Jeremy Affeldt | Derek Lowe | Brian Fuentes | 577 | 527 | 50 |
| 2006-08-10 | vs COL | 115 | W 4-3 | 59-56 | 1 | 48,699 | Chad Billingsley | Jason Jennings | Takashi Saito | Jose Mesa | | 581 | 530 | 51 |
| 2006-08-11 | vs SFN | 116 | W 3-2 | 60-56 | 1 | 53,695 | Mark Hendrickson | Noah Lowry | Brett Tomko | Mike Stanton | Jonathan Broxton | 584 | 532 | 52 |
| 2006-08-12 | vs SFN | 117 | W 6-5 | 61-56 | 1 | 46,444 | Brad Penny | Matt Cain | Brad Penny | Matt Cain | Takashi Saito | 590 | 537 | 53 |
| 2006-08-13 | vs SFN | 118 | W 1-0 | 62-56 | 1 | 55,699 | Greg Maddux | Jason Schmidt | Takashi Saito | Vinnie Chulk | | 591 | 537 | 54 |
| 2006-08-14 | vs FLO | 119 | W 4-2 | 63-56 | 1 | 44,749 | Derek Lowe | Dontrelle Willis | Derek Lowe | Dontrelle Willis | Giovanni Carrara | 595 | 539 | 56 |
| 2006-08-15 | vs FLO | 120 | W 4-0 | 64-56 | 1 | 47,960 | Chad Billingsley | Anibal Sanchez | Chad Billingsley | Randy Messenger | | 599 | 539 | 60 |
| 2006-08-16 | vs FLO | 121 | L 4-15 | 64-57 | 1 | 38,125 | Mark Hendrickson | Josh Johnson | Josh Johnson | Mark Hendrickson | | 603 | 554 | 49 |
| 2006-08-18 | @ SFN | 122 | L 3-7 | 64-58 | 1 | 42,862 | Brad Penny | Jason Schmidt | Jason Schmidt | Brad Penny | | 606 | 561 | 45 |
| 2006-08-19 | @ SFN | 123 | W 14-7 | 65-58 | 1 | 42,833 | Greg Maddux | Brad Hennessey | Greg Maddux | Brad Hennessey | | 620 | 568 | 52 |
| 2006-08-20 | @ SFN | 124 | W 5-2 | 66-58 | 1 | 42,052 | Derek Lowe | Matt Morris | Derek Lowe | Matt Morris | Takashi Saito | 625 | 570 | 55 |
| 2006-08-21 | @ SDN | 125 | L 2-4 | 66-59 | 1 | 33,244 | Chad Billingsley | Tim Stauffer | Tim Stauffer | Elmer Dessens | Trevor Hoffman | 627 | 574 | 53 |
| 2006-08-22 | @ SDN | 126 | L 0-1 | 66-60 | 1 | 32,774 | Mark Hendrickson | Jake Peavy | Jake Peavy | Mark Hendrickson | Trevor Hoffman | 627 | 575 | 52 |
| 2006-08-23 | @ SDN | 127 | L 2-7 | 66-61 | 1 | 36,613 | Brad Penny | Woody Williams | Woody Williams | Brad Penny | | 629 | 582 | 47 |
| 2006-08-25 | @ ARI | 128 | L 7-9 | 66-62 | 1 | 26,276 | Greg Maddux | Claudio Vargas | Brandon Lyon | Aaron Sele | | 636 | 591 | 45 |
| 2006-08-26 | @ ARI | 129 | W 4-3 | 67-62 | 1 | 40,358 | Derek Lowe | Miguel Batista | Jonathan Broxton | Luis Vizcaino | Takashi Saito | 640 | 594 | 46 |
| 2006-08-27 | @ ARI | 130 | W 6-3 | 68-62 | 1 | 30,337 | Chad Billingsley | Livan Hernandez | Chad Billingsley | Livan Hernandez | Takashi Saito | 646 | 597 | 49 |
| 2006-08-28 | vs CIN | 131 | W 6-5 | 69-62 | 1 | 44,176 | Brad Penny | Chris Michalak | Brad Penny | Chris Michalak | Jonathan Broxton | 652 | 602 | 50 |
| 2006-08-29 | vs CIN | 132 | W 6-5 | 70-62 | 1 | 44,697 | Mark Hendrickson | Eric Milton | Derek Lowe | Ryan Franklin | | 658 | 607 | 51 |
| 2006-08-30 | vs CIN | 133 | W 7-3 | 71-62 | 1 | 47,356 | Greg Maddux | Aaron Harang | Greg Maddux | Aaron Harang | | 665 | 610 | 55 |
| 2006-09-01 | vs COL | 134 | W 6-3 | 72-62 | 1 | 49,601 | Derek Lowe | Jason Jennings | Derek Lowe | Jason Jennings | Takashi Saito | 671 | 613 | 58 |
| 2006-09-02 | vs COL | 135 | W 14-5 | 73-62 | 1 | 48,984 | Brad Penny | Aaron Cook | Brad Penny | Aaron Cook | | 685 | 618 | 67 |
| 2006-09-03 | vs COL | 136 | L 5-12 | 73-63 | 1 | 44,895 | Aaron Sele | Byung-Hyun Kim | Byung-Hyun Kim | Aaron Sele | | 690 | 630 | 60 |
| 2006-09-04 | @ MIL | 137 | L 3-6 | 73-64 | 1 | 33,645 | Greg Maddux | David Bush | David Bush | Greg Maddux | Francisco Cordero | 693 | 636 | 57 |
| 2006-09-05 | @ MIL | 138 | L 0-9 | 73-65 | 1 | 13,427 | Mark Hendrickson | Doug Davis | Doug Davis | Mark Hendrickson | | 693 | 645 | 48 |
| 2006-09-06 | @ MIL | 139 | W 2-1 | 74-65 | 1 | 25,106 | Derek Lowe | Chris Capuano | Derek Lowe | Chris Capuano | Takashi Saito | 695 | 646 | 49 |
| 2006-09-07 | @ NYN | 140 | L 0-7 | 74-66 | 1 | 48,583 | Brad Penny | Tom Glavine | Tom Glavine | Brad Penny | | 695 | 653 | 42 |
| 2006-09-08 | @ NYN | 141 | W 5-0 | 75-66 | 1 | 52,077 | Hong-Chih Kuo | John Maine | Hong-Chih Kuo | John Maine | | 700 | 653 | 47 |
| 2006-09-09 | @ NYN | 142 | L 2-3 | 75-67 | 1 | 47,062 | Greg Maddux | Orlando Hernandez | Orlando Hernandez | Greg Maddux | Billy Wagner | 702 | 656 | 46 |
| 2006-09-10 | @ NYN | 143 | W 9-1 | 76-67 | 1 | 48,760 | Eric Stults | Steve Trachsel | Eric Stults | Steve Trachsel | | 711 | 657 | 54 |
| 2006-09-12 | @ CHN | 144 | L 8-9 | 76-68 | 1 | 35,618 | Derek Lowe | Sean Marshall | David Aardsma | Tim Hamulack | | 719 | 666 | 53 |
| 2006-09-13 | @ CHN | 145 | W 6-0 | 77-68 | 1 | 35,868 | Brad Penny | Angel Guzman | Brad Penny | Angel Guzman | | 725 | 666 | 59 |
| 2006-09-14 | @ CHN | 146 | L 5-6 | 77-69 | 1 | 31,361 | Hong-Chih Kuo | Wade Miller | Scott Eyre | Brett Tomko | Bob Howry | 730 | 672 | 58 |
| 2006-09-15 | vs SDN | 147 | W 3-1 | 78-69 | 1 | 52,911 | Greg Maddux | David Wells | Greg Maddux | David Wells | Takashi Saito | 733 | 673 | 60 |
| 2006-09-16 | vs SDN | 148 | L 2-11 | 78-70 | 1 | 55,781 | Chad Billingsley | Woody Williams | Woody Williams | Chad Billingsley | Brian Sweeney | 735 | 684 | 51 |
| 2006-09-17 | vs SDN | 149 | L 1-2 | 78-71 | 2 | 54,601 | Derek Lowe | Chris Young | Scott Linebrink | Jonathan Broxton | Trevor Hoffman | 736 | 686 | 50 |
| 2006-09-18 | vs SDN | 150 | W 11-10 | 79-71 | 1 | 55,831 | Brad Penny | Jake Peavy | Aaron Sele | Rudy Seanez | | 747 | 696 | 51 |
| 2006-09-19 | vs PIT | 151 | L 6-10 | 79-72 | 2 | 43,734 | Hong-Chih Kuo | Ian Snell | Ian Snell | Hong-Chih Kuo | | 753 | 706 | 47 |
| 2006-09-20 | vs PIT | 152 | L 4-6 | 79-73 | 2 | 46,319 | Greg Maddux | Shawn Chacon | Shawn Chacon | Greg Maddux | Salomon Torres | 757 | 712 | 45 |
| 2006-09-21 | vs PIT | 153 | W 5-2 | 80-73 | 2 | 48,567 | Chad Billingsley | Shane Youman | Chad Billingsley | Shane Youman | Takashi Saito | 762 | 714 | 48 |
| 2006-09-22 | vs ARI | 154 | W 2-0 | 81-73 | 2 | 43,990 | Derek Lowe | Claudio Vargas | Derek Lowe | Claudio Vargas | Takashi Saito | 764 | 714 | 50 |
| 2006-09-23 | vs ARI | 155 | L 3-9 | 81-74 | 2 | 49,791 | Brad Penny | Miguel Batista | Miguel Batista | Brad Penny | | 767 | 723 | 44 |
| 2006-09-24 | vs ARI | 156 | W 5-1 | 82-74 | 2 | 49,822 | Hong-Chih Kuo | Livan Hernandez | Takashi Saito | Luis Vizcaino | | 772 | 724 | 48 |
| 2006-09-26 | @ COL | 157 | W 11-4 | 83-74 | 2 | 20,133 | Greg Maddux | Jason Jennings | Greg Maddux | Jason Jennings | | 783 | 728 | 55 |
| 2006-09-27 | @ COL | 158 | W 6-4 | 84-74 | 2 | 18,858 | Derek Lowe | Aaron Cook | Derek Lowe | Aaron Cook | Takashi Saito | 789 | 732 | 57 |
| 2006-09-28 | @ COL | 159 | W 19-11 | 85-74 | 2 | 21,154 | Brad Penny | Byung-Hyun Kim | Mark Hendrickson | Ray King | | 808 | 743 | 65 |
| 2006-09-29 | @ SFN | 160 | W 4-3 | 86-74 | 1 | 42,587 | Hong-Chih Kuo | Noah Lowry | Jonathan Broxton | Mike Stanton | Takashi Saito | 812 | 746 | 66 |
| 2006-09-30 | @ SFN | 161 | W 4-2 | 87-74 | 1 | 42,769 | Greg Maddux | Matt Cain | Greg Maddux | Matt Cain | Takashi Saito | 816 | 748 | 68 |
| 2006-10-01 | @ SFN | 162 | W 4-3 | 88-74 | 1 | 42,831 | Eric Stults | Jason Schmidt | Chad Billingsley | Brad Hennessey | Joe Beimel | 820 | 751 | 69 |