The Jets extended their winning streak to four games and ended Philadelphia's at three.
Scott Hartnell and Wayne Simmonds scored for the Flyers.
The Jets came out fast and Byfuglien scored a power-play goal at 5:36 of the first period, as he snapped the puck past Steve Mason.
It was only Winnipeg's seventh power-play goal this season as the team is 30th in the NHL with the man advantage.
But the Flyers came back with Hartnell's wraparound at 6:25 that was ruled a goal after a review. Jets goalie Ondrej Pavelec appeared to move it past the goal line with his glove.
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