The Panthers ended a five-game losing streak and handed the Flyers their first setback in three outings.
Florida took a 3-0 lead after one period with Huberdeau producing the last of those three goals by converting his penalty attempt. Peter Mueller and Tomas Kopecky scored in a span of 29 seconds earlier in the opening period to put the Panthers in front for good.
Huberdeau tipped in a shot midway through the second period, knocking Philadelphia goaltender Ilya Bryzgalov out of the game.
Florida's final goal came from Peter Mueller with 5:27 left in the contest.
Scott Clemmensen stopped 32 shots to get the victory. It was his first win of the year after suffering three losses, two of them in overtime.
Bryzgalov allowed four goals on 15 shots before being replaced by Brian Boucher.