After the Braves' 8-5 loss that gave Houston a 2-1 lead in the series, Thomson said he won't pitch again this season.
"If I cough, take a deep breath or turn the wrong way, it hurts," Thomson said. "They said it will take six to eight weeks to get back where it should be."
Thomson left his final regular-season start Oct. 2 at the Chicago Cubs after just three innings because of the same problem.
After Thomson threw a 2-0 pitch to Jeff Bagwell, Houston's third batter, Braves manager Bobby Cox came out of the dugout with a trainer. They talked briefly with the right-hander and then brought in Paul Byrd to pitch.
"It didn't hurt in the bullpen, and it didn't hurt when I was getting ready," Thomson said. "It just popped."
Thomson set a career high with 14 wins, including a six-game-winning streak to end the regular season.
Astros leadoff hitter Craig Biggio grounded out on the first pitch, and Carlos Beltran hit the second pitch off the left-center field wall for a double. Byrd threw two more balls to Bagwell, a walk charged to Thomson, but then got out of the first without allowing a run.