Red Sox manager John Farrell said Pedroia's injury swelled up in the subsequent innings, limiting his range of motion.
"The pitch hit in the left lat area, left rib cage. It continued to swell and tighten up," Farrell said. "He was losing a lot of range of motion with the left arm, so we had to get him off his feet. We'll have a better read once he goes through the exam here at the local hospital."
Pedroia was the second batter hit by Astros pitcher James Hoyt in the seventh inning. Hoyt plunked Mookie Betts in the right knee in the previous at-bat. Plate umpire Greg Gibson issued warnings to both benches after Pedroia glared and yelled at Hoyt. Both managers came onto the field as Pedroia continue to scream and point at the mound before calming down and heading to first base.
ESPN's Scott Lauber and The Associated Press contributed to this report.