Pence grounded out to third for the first out in Houston's three-run first inning, and was replaced in right field by Brian Bogusevic in the bottom of the inning.
Pence is hitting .280 with 24 home runs and a career-high 85 RBIs in 145 games. He snapped an 0-for-13 slump with a ninth-inning single in Monday's 8-2 win against the Nationals.
Pence said he's dealt off and on with a hip flexor for some time, but exacerbated the problem area by running too hard to first base on his first-inning grounder.
"I've dealt with it my whole career," he said. It was bugging me a little bit, but I think I pushed a little too hard on that run to first, and that's what got it more than you can play on."
On the way back to the dugout, he knew the hip would prevent him from running hard in the outfield.
"When you tweak something like that, you can't run through it," Pence said. "It's impossible. I knew that I wasn't going to be capable to sprint again. I would have had to jog, and that's not acceptable in the outfield."
Pence expects to miss two or three days, but manager Brad Mills said he would be re-evaluated before Wednesday's third game of the four-game series at Nationals Park. For now, Mills considers Pence day-to-day.
"It might be a couple of days," Mills said. "We'll just have to see how it is. We'll check him in the morning and probably know a little bit more tomorrow."