Bregman doubled to lead off the sixth and advanced to third on a 5-3 groundout by Tyler White. After reaching third, Bregman appeared to be grabbing at the hamstring, which prompted manager A.J. Hinch to remove him from the game after a brief discussion.
"It was actually an excellent baserunning play," Hinch said. "He pulled up."
The former No. 2 overall pick, who was replaced by fellow rookie Tony Kemp, is hitting .260 in his rookie campaign.
Neither he nor Altuve is expected to play on Friday, when the Astros begin a series in Seattle.
"They're getting looked at, getting all the tests [from] doctors," Hinch said. "They're going to have a full evaluation before we're going to know anything, but I'm not optimistic about Friday for either of them."
Jordan Ray is a reporter for MLB.com based in Houston. This story was not subject to the approval of Major League Baseball or its clubs.