Jagr scored with 3:12 left in the second period, putting the Flyers ahead to stay at 2-1, and added an assist.
Ilya Bryzgalov started in net and stopped 14-of-16 shots, but departed nearly 7 minutes into the third period with an undisclosed injury. He was replaced by Sergei Bobrovsky, who turned aside the three shots he saw.
NHL points leader Claude Giroux of Philadelphia also left the game after two periods with an undisclosed injury.
Mathieu Garon made 27 saves in the setback.
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