Pedroia was hit in the rib area with a 92-mph pitch in the seventh inning of Boston's 6–5 win by Astros James Hoyt.
Pedroia yelled at Hoyt before being heading to first base and ended up leaving the game for good a short time later.
"The pitch hit him in the left lat area, left rib cage," Red Sox manager John Farrell said. "It continued to swell and tighten up. He was losing a lot of range of motion with his left arm, so we had to get him off his feet. But we'll have a better read once he goes through the exam here at a local hospital."
Hoyt also hit Red Sox rightfielder Mookie Betts in the right knee in the previous at-bat.
It is not known if Pedroia will be available for the team's three-game set that starts in Kansas City on Monday, although he was cleared to fly with the team.
Pedroia is hitting .296 with two home runs and 25 RBI for this season for Boston (39–30), who are tied with the New York Yankees for AL East lead.