Mike Knuble's goal with 1:24 left in regulation forced overtime, and Simon Gagne had three goals, including a pair on the power play, for Philadelphia, which has the fewest wins (13) and points (34) in the NHL.
Held scoreless during regulation, Crosby, the league's scoring leader, beat Antero Niittymaki on the Penguins' third shot in the shootout. Marc-Andre Fleury then stopped Gagne to win it.
With Niittymaki pulled from the net, Knuble redirected Alexei Zhitnik's slap shot in to tie 4-4.
Mark Recchi and Erik Christensen scored 30 seconds apart early in the third period, and Jordan Staal and Michel Ouellet also had goals for the Penguins, the NHL's most improved team this season. Pittsburgh has won 10 of 12 with two overtime losses.
The Flyers haven't won at home since beating former coach Ken Hitchcock in his debut with Columbus on Nov. 24, and have just three victories there in 25 games.