It was the second career hat trick for Pavelski, who led the charge as San Jose came back from the Olympic break with a big win.
Alex Stalock turned aside 27 shots for the Sharks, who recorded a third straight victory.
Matt Read, Brayden Schenn and Andrej Meszaros each had a goal for the Flyers.
Steve Mason started in goal but was pulled after allowing four goals on 16 shots.
Ray Emery stopped 11-of-14 the rest of the way.