Three straight singles from Ryan Theriot, Jon Jay and Albert Pujols loaded the bases with no outs off Danys Baez (1-2) in the ninth. After Theriot was forced at home on Matt Holiday's grounder, J.C. Romero came on to pitch to Berkman.
The switch-hitter lofted the first pitch over the drawn-in outfield into center, scoring Jay with the winning run and giving the Cards a two-game series sweep against the Phillies.
Fernando Salas (2-0) got the win with a scoreless top of the ninth. St. Louis starter Jamie Garcia allowed only one unearned run on five hits over eight frames.
Placido Polanco's sacrifice fly in the eighth -- set up by second baseman Tyler Greene's fielding error -- forged a 1-1 tie for Philadelphia.