That took Lee off the hook. Lee allowed three earned runs in six innings, striking out seven and walking two.
The Phillies went ahead, 4-3, in the eighth inning.
Juan Pierre and Hunter Pence hit consecutive singles against Jon Rauch to begin the inning, putting runners at the corners. Ty Wigginton struck out for the first out.
Shane Victorino then hit a sacrifice fly to center. Pierre beat the accurate but weak throw home from Andres Torres.
The Phillies went on to score six runs in the ninth inning on Jimmy Rollins' three-run homer, Wigginton's RBI double, and Victorino's two-run single.
The Mets had taken a 1-0 lead on David Wright's first-inning RBI double. Daniel Murphy, who walked, scored on a close play at the plate.
Wright hit a shot that Victorino played well off the center-field wall. Victorino hit cutoff man Rollins, who threw a strike to the plate. Murphy, who went though the stop sign of third base coach Tim Teufel, was called safe by home plate umpire Ed Rapuano, eluding Schneider's tag.
Wigginton, a former Met, tied the score in the second with a towering home run to left off starter Dillon Gee.
It was Wigginton's second home run of this series and fifth of the season.
In the Phillies' sixth, Rollins led off with a single. Pierre then beat out a bunt for a single, putting runners on first and second. On the play, Gee should have let the ball roll foul instead of attempting to make the play on Pierre.
Pence then grounded into a 6-4-3 double play. After a walk to Wigginton, Victorino ended the inning with a groundout.
In the bottom of the sixth, the Mets took a 3-1 lead on Lucas Duda's two-run homer to right-center field. Duda crushed a first-pitch 91-m.p.h. fastball from Lee, knocking in Scott Hairston, who had hit a one-out double.
Winning pitcher Antonio Bastardo and Jose Contreras threw scoreless seventh and eighth innings, respectively, for the Phillies. Raul Valdes allowed three runs in two-thirds of an inning before Jonathan Papelbon got the game's final out.
Contact Marc Narducci at 856-779-3225 or firstname.lastname@example.org. Follow @sjnard on Twitter.