Voracek and linemate Claude Giroux forced a Dustin Byfuglien turnover behind the Winnipeg net, and Voracek slid the puck through Ondrej Pavelec's pads for the win.
Marc Streit and Vincent Lecavalier added goals for the Flyers, who came back from a 3-1 deficit.
Matt Halischuk, Mathieu Perreault and Byfuglien scored for the Jets.
Philadelphia (13-14-6) followed up their 7-4 Saturday night win over Toronto to improve to 5-9-3 on the road.
The Jets (17-10-7) saw a two-game winning streak come to an end.
Lecavalier tied the game with 3:14 remaining, seconds after an offensive zone faceoff, with a high shot over Pavelec's blocker after a failed clearing attempt by Winnipeg defenceman Jay Harrison.
Rob Zepp, a 33-year-old from Newmarket, Ont., made his first career NHL start for the Flyers and stopped 25-of-28 shots, including a sprawling toe save off Mark Scheifele late in the second period. Called up from Lehigh Valley of the American Hockey League due to an injury to regular starter Steve Mason, Zepp spent the previous seven seasons in Germany, and two years before that in Finland.
Pavelec made 19 saves for Winnipeg.
The Jets played for a second game without their top four defencemen, all of whom are out until at least January. Byfuglien, who was moved back to his natural position on the blue-line after starting the season as a forward, led the team with almost 27 minutes of ice time.
Voracek opened the scoring after just 46 seconds of play as he one-timed a pass from Claude Giroux on a two-on-one rush for his 13th goal of the season. Voracek's 44 points give him the league lead, two better than Tyler Seguin of Dallas.
Halischuk's slap shot from the top of the right faceoff circle — his first of the season — tied the game six minutes later.
Byfuglien gave the Jets the lead 55 seconds later when he drove in from the right point, cut to the front of the net and shovelled the puck over Zepp's shoulder.
Winnipeg held a 17-9 shot advantage after the first period.
Perrault scored at 11:21 of the second period, corralling the rebound from a Michael Frolik shot at the side of the net and putting it past Zepp to make it 3-1.
The Flyers had four minutes of power-play time late in the frame, but couldn't find the net.
Streit's point shot through traffic beat Pavelec to the stick side to make it 3-2 with 13:54 remaining.
The Flyers thought they had scored early in the third period when Chris VandeVelde's shot beat Pavelec and the referee declared it a goal. But video review showed the puck hit the crossbar and came straight down without crossing the goal-line.
Notes: The Flyers were playing their second contest of an eight-game road trip as Disney on Ice takes over the Wells Fargo Center. They play in Minnesota on Tuesday, and don't play again at home until Jan. 6. … The Jets alternated goalies for the 13th straight game. Rookie Michael Hutchinson leads the NHL with a .940 save percentage and a goals-against average of 1.73.