Manager Mike Scioscia said the star will be sidelined for "a significant amount of time."
Pujols has a partially torn plantar fascia, an injury that has bothered him most of the season. He aggravated it while running out a single in the ninth inning of Friday's 6-4 loss to Oakland.
"This is something that, talking to Albert, has been going on for six or seven years," Scioscia said before the Angels' game against Athletics. "It's been going on for a long time and he's managed it. This is a big blow to our team right now."
Although surgery seems unlikely, Scioscia didn't rule out the possibility that Pujols could be sidelined for the rest of the year.
Pujols left the team and returned to Los Angeles on Saturday morning for additional testing. That's when the injury was diagnosed.
"We'll just take it one step at a time and see how it goes," Scioscia said. "But this is not something that's going to heal in a week or two. After that we'll just wait and get direction from our medical department and how Albert feels. It's a significant amount of time, that's what it's going to take."
The three-time NL MVP, who signed a $240 million, 10-year contract with the Angels as a free agent in December 2011, has served as the club's designated hitter most of the season. Pujols was hitting .258 with 17 home runs and 64 RBIs before re-injuring his foot.
The Angels went into the season with hopes of winning the AL West. They began the day with a 48-54 record, 12 games behind the first-place A's.
Outfielder Kole Calhoun was called up from Triple-A Salt Lake.