The first baseman injured his calf while running out a ground ball during a 7-2 victory over the Cincinnati Reds on Tuesday night. He flew to St. Louis for tests that indicated a strain rather than a severe tear, as initially feared.
He will start therapy in the next few days. The Cardinals want to be sure the calf is fully healed before he plays again.
The Cardinals also put right-hander Adam Wainwright on the 15-day disabled list Wednesday. He sprained the middle finger on his pitching hand during his start Saturday in Houston, and lasted only five innings.
Chris Duncan was recalled from Triple-A Memphis and was in Pujols' spot at first base for a game against the Cincinnati Reds.
Pujols had to be helped off the field on Tuesday night. He took a few steps out of the batter's box before stopping and grabbing the calf, which had bothered him earlier in the season.
The Cardinals feared that he might have torn the muscle, which would have meant an extended absence. He flew back to St. Louis for tests on Wednesday that indicated the injury is less severe.
"The first indication is that it's not the scenario that would have kept him out for six weeks to two months," manager Tony La Russa said. "We're holding our breath."
There's no indication how long the Cardinals' top hitter might be sidelined. Pujols also missed time last season because the calf was tight and sore.
"It's the second time it's happened, so we need to get him well," La Russa said. "Going back to last year, it's the third time. We'll just try to get it 100 percent healed."
Pujols is batting .347 -- third-best in the National League -- and leads the team with 16 homers. He has driven in 42 runs, second to Ryan Ludwick's 50 RBIs.
He will likely go on the disabled list to open a roster spot for Joel Pineiro, who is expected to come off the disabled list Thursday and start the final game of the series in Cincinnati. Pineiro has been sidelined since May 21 with a groin strain.
The Cardinals are 39-27 despite all of their injuries.
Right-hander Todd Wellemeyer had to skip a start because of elbow inflammation, but is expected to pitch against Philadelphia over the weekend. Rick Ankiel missed five games with an infected right knee, but rejoined the Cardinals on Tuesday for the start of the series.