The Thrashers closed within four points of the eighth-place Buffalo Sabres in the playoff race with their second win in six days over the Eastern Conference-leading Flyers. Atlanta will face Buffalo on Saturday.
Danny Briere scored two goals, including a tying shot with 1:17 left in regulation for the Flyers, who overcame three one-goal deficits.
But goals by Schremp and Wheeler in the shootout finally gave the Thrashers a lead that couldn't be overcome. Ondrej Pavelec blocked Philadelphia's first attempt by Mike Richards, and Briere fired wide in the second round.