Brett Wallace, who was recalled from Triple-A Oklahoma City, flew to Houston on Sunday morning and was in the lineup for the series finale against the Reds.
The only other time Lee has been on his disabled list in his 13-year career was when he broke his finger in August 2008.
"It's very disappointing, because you want to be out there and be in the game," Lee said. "Right now, all we can do is get treatment, and I think that this week, before we go on the road, the doctor is going to look at it again and see how it's progressing."
Lee injured the hamstring running to first base in the eighth inning of Friday's game. He said it's getting better, but it's going to be a few days before he can even start doing baseball activities.
"When it happened, it was pretty sore," he said. "Coming into today, I'm not healthy, but I can walk better now and I have a normal stride. I guess it's improving."
Wallace was hitting .265 with nine doubles, 10 home runs and 37 RBIs in 50 games for the RedHawks. He hit three homers and had eight RBIs in the last four games for Oklahoma City, including a grand slam on Saturday.
"It's great to be back with the guys," Wallace said. "It was kind of unexpected, but I'm glad to be back and hopefully I can help."
Last season, Wallace hit .259 with 22 doubles, five home runs and 29 RBIs in 115 games with the Astros, for which he has appeared in 166 games the past two years. Astros manager Brad Mills said Wallace will get the bulk of the starts at first with Lee on the shelf.
"He's swinging the bat really well, and hopefully we can catch up in that breeze as we move forward," Mills said. "Watching him today, he looks good swinging the bat and physically he looks good. I would encourage him to continue to do that."
On Saturday, the Astros placed backup outfielder Travis Buck on the disabled list with a strained Achilles and recalled Fernando Martinez from Oklahoma City.