The Sharks won for the sixth time in their seven games this season while the Flyers remained winless in six outings. Three of the Philadelphia losses have come in overtime or in a shootout.
San Jose also defeated the Flyers last Saturday in overtime 5-4. The Sharks became the first team in the Western Conference to reach the 12-point mark this year.
The teams combined for seven goals in the first period, at the end of which San Jose owned a 4-3 lead.
Patrick Marleau's fourth goal of the season put the Sharks in front 6-4 early in the third period, but Joffrey Lupul scored for the second time in the game to draw the Flyers within one.
Daniel Briere produced a power-play goal with 65 seconds remaining in regulation to tie it.
San Jose's Evgeni Nabokov allowed six goals on 29 shots during regulation and overtime, but stopped the only two attempts he saw in the shootout to ensure the victory.
Marleau scored twice and had two assists.