The Jets have won six straight games in Philadelphia, including four when they were the Atlanta Thrashers, since a 5-3 loss on Jan. 21, 2009. The franchise has beaten the Flyers in nine of the last 10 meetings.
Chris Thorburn scored his first goal in nearly a year for Winnipeg's lone tally in regulation.
Brayden Schenn scored for Philadelphia in the first period. The Flyers have gone to a shootout in three straight games, winning one.
Ondrej Pavelec stopped Sean Couturier, Claude Giroux and Jaromir Jagr in the shootout.
Ilya Bryzgalov had allowed goals on all five shootout attempts he'd faced before stopping Kyle Wellwood and Blake Wheeler. But Little slid one under Bryzgalov's pads to win it.
The teams combined for 27 goals in their two previous meetings, including Winnipeg's 9-8 victory at the Wells Fargo Center on Oct. 27. But this was hardly the same. Neither club registered a shot until the Jets took one on Bryzgalov 10:36 into the first.
The victory was Winnipeg's fourth in 13 games since the calendar turned to 2012.
Pavelec stuffed All-Star Scott Hartnell on a 2-on-1 breakaway to keep it 1-all with 8:38 left in the third period, and it stayed tied the rest of the way.
Schenn gave the Flyers a 1-0 lead with 4:49 left in the first period when he scored his fourth goal of the season during a power play. Matt Carle took a crossing pass from Jagr and fired a shot at Pavelec. The rebound bounced in front and Schenn took a few whacks at it until it slid between Pavelec's pads.
The Flyers nearly went up 2-0 a minute later, but Pavelec made a glove save on a point-blank shot by Couturier.
Winnipeg tied it when Thorburn scored his first goal in 60 games early in the second period. Thorburn's wrister from the slot sailed past Bryzgalov for his first goal since March 19, 2011, against Buffalo.
Jagr almost put the Flyers back ahead a few minutes later, but his one-timer hit the crossbar.
Notes: Jagr was back in the lineup after missing two games with a groin injury. ... The Flyers are 30-10-7 against Winnipeg/Atlanta since it joined the NHL in 1999. They were 29-3-1 against the franchise from 1999-2009. ... The Flyers fell to 11-8-3 at home. ... Giroux, who entered the game second in the NHL in points, hasn't scored a goal in 12 games. ... Thorburn followed his goal with a spirited fight against Tom Sestito in the third period. ... The Flyers are 1-7-3 against the Winnipeg franchise since a 14-game winning streak from 2003-09.