Collin McHugh (3-2) allowed one run and five hits with five strikeouts in five innings for Houston. It was the right-hander's first outing since detaching a fingernail on his pitching hand Sept. 8.
McHugh has made only 10 starts this season after also missing time with a shoulder issue.
Altuve went the other way for his 24th home run, a solo shot to right field in the fourth. Bregman knocked in Marwin Gonzalez later in the inning to give the Astros a 2-1 lead.