Braun appeared to be in pain after swinging and missing in his final at-bat in the sixth. He walked gingerly back to the dugout after the strikeout. Gabe Kapler replaced Braun.
"Yeah, I'm fine," Braun said. "I'm good."
Milwaukee manager Ned Yost was less sure.
"It was stiff and tight, and it was getting tight after that last swing, so I put 'Kap in there,'" Yost said. "I'll see how he feels tomorrow, but this is something I am not really interested in playing around with. I am not going to go out here and go through this every night."
Braun pinch hit Saturday and returned to the lineup Sunday against the Los Angeles Dodgers. He batted four times against the Astros on Monday, striking out twice.
The slugger came in batting .301 with a team-best 32 home runs and 86 RBI.
Meanwhile, Rickie Weeks was out of the lineup after leaving Sunday's game with a sprained left thumb. Weeks saw team doctor William Raasch on Monday, and he confirmed the diagnosis. Weeks is day to day.