Holliday has a contusion on the elbow and is considered day to day.
"He just got hit in a bad spot. Everything came out negative," Cardinals manager Mike Matheny said.
Shane Robinson replaced Holliday as a pinch-runner, staying in the game to play the outfield.
Holliday, who has 27 homers and 100 RBIs, is in an 0-for-10 skid.
Holliday appeared to take the pitch on the point of his elbow, and after being attended to by Matheny and Cards trainers, left the game.
Steve Overbey is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.