Philadelphia's Wayne Simmonds sent the game into the extra period with a goal with 10 seconds left in regulation.
Ilya Bryzgalov made 22 saves in the victory for Philadelphia (33-19-7). Claude Giroux had a goal and two assists, while Scott Hartnell added a goal and an assist. Maxime Talbot also scored for the Flyers.
Ondrej Pavelec made 50 saves for Winnipeg (29-26-7).
Evander Kane made it 4-3 for the Jets at 4:57 of the third period on the power play.
Andrew Ladd scored a pair of goals 64 seconds apart and Dustin Byfuglien had a goal and an assist for Winnipeg. Tim Stapleton added three assists and Bryan Little added two.
Winnipeg was 3 for 3 on the power play and Philadelphia was 1 for 3.
Byfuglien got things going with his ninth goal of the season on the power play when Talbot was in the penalty box for cross-checking.
Little sent a pass across the ice to Byfuglien, who fired a one-timer that went over Bryzgalov's stick at 12:31.
Giroux tied it three minutes later when he flipped in a backhand as Pavelec was trying to stretch back across the crease.
Philadelphia made it 2-1 at 1:08 of the second period with Harnell's 28th of the season. His team-leading goal came off a rebound 11 seconds after Jets defenseman Tobias Enstrom was called for interference.
Winnipeg responded with Ladd's two quick goals. The first came on the power play at 7:52 and was followed by his 19th of the season on a backhand past Bryzgalov at 8:56.
Philadelphia quickly tied it 3-3 at 11:14 on a close shot by Talbot.
Blake Wheeler assisted on Ladd's first goal to extend his points streak to four games (one goal, eight assists).
Kane put the Jets up 4-3 in the third period on a long, high shot that Bryzgalov couldn't grab with his glove.
It was the last of four games this season between the Jets and Flyers, with Winnipeg finishing 3-0-1.
The teams combined for a total of 39 goals in those games, including a 9-8 Jets' win on Oct. 27 that was the highest-scoring NHL game in the past 15 years.
Notes: Jets forward Antti Miettinen played his 500th game. He was claimed off waivers by Winnipeg, his third NHL club, in December. ... Tuesday marked the third of an eight-game homestand for the Jets, who host Tampa Bay on Thursday. The Flyers travel to Edmonton on Thursday for the second of their four-game road trip.