Pascal Dupuis, James Neal and Tyler Kennedy also scored goals for the Atlantic Division-leading Penguins, who won their third straight game.
Jakub Voracek had two power-play goals, Zac Rinaldo and Kimmo Timonen also scored for the Flyers, who blew a 4-1 lead after the first period.
Both starting goalies - Philadelphia's Ilya Bryzgalov and Pittsburgh's Marc-Andre Fleury - were pulled after allowing four goals.
Scott Hartnell had his tying goal disallowed near the midpoint of the third period because his stick was above the crossbar when he deflected Timonen's shot into the net.
The Flyers fell to 11-13-1 and remain on the outside of the playoff race with 23 games remaining.