Bregman left Wednesday night's 13-6 win over the Colorado Rockies after favoring his right leg while running out a double to lead off the fourth inning. He limped into second base and immediately was removed from the game.
"I felt it when I was running down the line to first base, right about when I was going to make the turn to second,'' Bregman said after the game. "Disappointed. I want to be out there every day, playing with my guys. I was starting to feel pretty damn good."
Baker told reporters that Bregman is returning to Houston to undergo an MRI.
Bregman, a two-time All-Star, is hitting .272 with four home runs and 14 RBIs this season.
Abraham Toro, who replaced Bregman on Wednesday, is playing third base for the Astros in Thursday's game against the Rockies.
Left-handed reliever Cionel Perez is being activated to replace Bregman on the active roster. Perez has a 6.64 ERA over 13 appearances for Houston over the past two seasons.
Information from The Associated Press was used in this report.