It was just the second time in 67 games this season that Pujols was not batting third and playing first base for the Cardinals, who entered play one game behind the Milwaukee Brewers for first place in the NL Central.
"It's a good day for him [to rest]," manager Tony La Russa said. "He was sick last week, and we didn't give it to him. It's just a good time for it."
The temperature in St. Louis reached 96 degrees on Thursday, forcing the Cardinals to cancel batting practice, instead hitting in the indoor cages.
Chris Duncan got the start at first base in place of Pujols, who La Russa said was also dealing with a sore ankle but could have played if needed.
B.J. Rains is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.