The Flyers have won four of their last five contests.
Jamie Drysdale scored the other goal the Flyers.
Ivan Fedotov turned aside 30 shots for Philadelphia, who moved to 27-26-8 on the season.
Mark Scheifele scored for the Jets, who dropped their second straight game.
Connor Hellebuyck stopped 30 shots for Winnipeg, who moved to 42-16-3 on the season.
Mark Scheifele got Winnipeg on the board halfway through the first period when he converted a slick backhand pass from Gabriel Vilardi past Fedotov to make it 1-0 Jets.
The goal was his 34th of the season.
Jamie Drysdale tied the contest 3:48 into the second when he worked a give-and-go with Noah Cates along the blue line before moving in from the top of the face off circle before unleashing a wrister which beat Hellebuyck to make it 1-1.
The goal was his 4th of the season.
There was no scoring in the third period.
Winnipeg had a chance to take the lead late in the third when Flyers defencemen Jamie Drysdale and Rasmus Ristolainen both took obstruction penalties but the Jets were unable to score.
The game remained tied and went to overtime.
There was no scoring in overtime and the game went to a shootout.
SHOOTOUT-PHILADELPHIA-Konecny (miss), Michkov (score)
WINNIPEG-Scheifele (miss), Connor (miss), Vilardi (miss).
SHOTS-PHILADELPHIA 32 WINNIPEG 31
ATTENDANCE-14,436
