The homer, Pujols' major league-leading 44th this season, led off the top of the 10th when he batted for third baseman Khalil Greene.
Andy LaRoche's sixth-inning error pulled St. Louis into a 1-1 tie with one out in the top of the sixth.
The winner for the Cardinals, who have won seven of eight, was Blake Hawksworth (2-0). Closer Ryan Franklin earned his 37th save despite walking two batters in the bottom of the tenth.
Pittsburgh's run scored on a fourth-inning double by Lastings Milledge.
He and Garrett Jones had two hits for the Pirates, who have lost nine in a row.
The losing pitcher was closer Matt Capps (3-8).
Copyright 2009 by United Press International.
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