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.
Fan, follow and download: Get the latest from NBCPhiladelphia.com anytime, anywhere. Follow us on Twitter, Facebook and NBC Philadelphia. Sign up for our sports newsletter. And, get breaking news delivered right to your mobile phone -- just text PHIBREAKING to 639710 to sign up. (Message and data rates may apply.)