After the Flyers took their three-goal advantage into the third period, Florida made it interesting with scores from Rostislav Olesz and David Booth.
Sergei Bobrovsky was perfect the rest of the way, however, and Danny Briere clinched it with his empty-net goal coming just 22 seconds from the end of the game. It was Briere's 28th of the season and he had two assists.
Philadelphia won for the fifth time in six games, getting 33 saves from Bobrovsky.
Tomas Vokoun stopped 31-of-34 shots to take the loss.
Philadelphia has won two of the three meetings between the teams this season with one remaining.