Manager Tony La Russa said he felt Pujols needed a day off. The Cardinals are off Monday, giving Pujols a two-day break.
The three-time NL MVP has been a healthy scratch twice this season, the last on July 20 against the New York Mets.
Lance Berkman made his 16th start at first on Sunday and collected three walks and scored three times.
Pujols, who has started 113 games at first this season, missed 13 games with a fractured wrist from June 20-July 4.
Information from The Associated Press was used in this report.