"Kaz's back tightened up a little bit on him," said Astros manager Cecil Cooper. "He'll be day-to-day, probably."
Matsui had told Cooper his back was a bit stiff before the game but said he was OK to play, but the tightness got worse during the first inning.
Mark Loretta replaced Matsui at second, batting leadoff.
Matsui was previously on the 15-day disabled list for a strained right hamstring in late June and also missed time earlier this season with anal fissures.
Krysten Oliphant is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.