"He's just sore from getting crashed by Hunter," said Astros manager Cecil Cooper. "I think the catcher's knee got him in his leg, and then Hunter came into his back a little bit."
Loretta had a heating pad on his left hamstring before Sunday's game.
He was supposed to be in the lineup against Oliver Perez, but Ty Wigginton will take his place at third base.
Cooper said Loretta could still pinch-hit if needed.
"We had to make a change this morning," Cooper said. "In an emergency, if I needed him, he could bat. But he's an older guy, and you've kind of got to be careful with those guys."
Michael Bourn, meanwhile, was again out of the starting lineup, his seventh game on the bench since spraining his right ankle on July 26 in Milwaukee.
Bourn pinch-hit in the 10th inning of Saturday's game and struck out swinging.
It was his second appearance in a game since the injury, both as a pinch-hitter. Cooper used David Newhan as a pinch-runner for Brad Ausmus in the ninth, a place where Bourn normally would have been used.
Cooper said he probably would have chosen to use starting pitcher Brandon Backe as a pinch-runner before putting Bourn on the bag.
"He's still not there yet," Cooper said. "He's a pinch-hitter at best at this point in time, and maybe an emergency guy."
Krysten Oliphant is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.