Late game bursts in the seventh, eighth, and ninth innings produced six runs for the Phillies as they went on to win 10-6.
Jimmy Rollins had three hits, one of which was a homerun in the top of the ninth that drove in three runs and solidified Philadelphia's lead.
Right fielder Lucas Duda drove in two runs for New York on a home run off of Lee in the bottom of the sixth.
The Phillies move to 27-25, helping gain on their division rival Mets.
Tomorrow Kyle Kendrick faces off against Mark Buehrle, as the Phillies travel back to Citizens Bank Park to take on the Miami Marlins.