Holliday, batting .264 with three home runs and 29 RBIs, was originally in the lineup at designated hitter, batting third. He was replaced by Yadier Molina.
Molina, who was the DH in Friday's series opener, was held out of the lineup Saturday for what manager Mike Matheny called a mental break.
Molina began the day Sunday batting .293 with five homers and 23 RBIs, but had just three hits in his previous 29 at-bats.
Molina went 1-for-3 Sunday and the Cardinals defeated the Blue Jays 5-0, winning back-to-back games for the first time since May 24 and 25 vs. Cincinnati.
St. Louis is off Monday before beginning a three-game series at Tampa Bay on Tuesday. Matheny said some of the Cardinals' team's doctors were already scheduled to meet the team in Florida, including their back specialist, and would examine Holliday before Tuesday's game.
"He's already walked by and said he's going to be fine,'' Matheny said.
The Associated Press contributed to this report.