Chad Durbin (4-1) held the Padres scoreless in the 11th and 12th innings to get the win.
The Phillies opened the scoring in the third inning when Rollins and Polanco put together back-to-back singles and Chase Utley drove in Rollins with a single to center field. The Padres tied it in the bottom of the third on a lead-off home run by Yorvit Torrealba.
Philadelphia went up 2-1 in the eighth when Raul Ibanez drove in Utley with a one-out single. The Padres made it 2-2 in the bottom of the ninth when pinch-runner Jerry Hairston scored from third on a two-out, bases-loaded balk by Phillies reliever Brad Lidge.
Ernesto Frieri (0-1) took the loss in relief for the Padres.