The Flyers (6-7-1), coming off a 5-2 loss in Toronto, won on the road for the second time this season. Jakub Voracek had two assists.
Andrew Ladd scored both goals for the Jets (5-6-1), the last in the final seconds. Winnipeg was coming off a 1-0 win in Ottawa on Saturday.
Ilya Bryzgalov was solid in net for the Flyers, who were outshot 26-23.
Al Montoya recorded his first loss as a starter for the Jets. Ondrej Pavelec replaced Montoya in the third after what was reported as a lower-body injury for Montoya.
The Flyers took a 2-1 lead in the first, even though they were outshot 9-6 by the Jets.
Montoya didn't have much of a chance when Schenn redirected Voracek's pass right in front of the net on Philadelphia's second shot of the game at 8:07.
Winnipeg tied it up at 14:12, when Blake Wheeler fed Ladd just in front of the Flyers net and he squeezed one past Bryzgalov's short side.
A late cross-checking penalty to defenseman Zach Redmond was costly, with Timonen slamming the puck down a clear path between the faceoff circles that Montoya wasn't fast enough to block.
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There was no scoring in the second, although Winnipeg again outshot the Flyers 10-6 for the period. There was also a short scrap between Jets defenseman Mark Stuart and McGinn.
McGinn then redirected Vortacek's pass into Winnipeg's net at the 4:17 mark from just outside the crease.
Ladd scored his final goal at 19:13 after the Jets pulled their goaltender.
The Jets went 0 for 4 on the power play.
This was Winnipeg's and Philadelphia's first meeting this season.
It was also the first game defenseman Dustin Byfuglien has played since the Jets visited Montreal. He got a massive cheer when his name was announced in the starting lineup.
NOTES: The Jets went into the game with the most productive defense in the NHL at 34 points, led by top-scorer Tobias Enstrom with 13 points.
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