Pavelec stopped all 17 shots he saw in the second period with Winnipeg clinging to a 1-0 lead and wasn't dented until 3:16 into the final frame, when Shawn Thornton tipped in a pass from Daniel Paille.
The Jets responded 1 1/2 minutes later when Little collected the puck after a face-off at center ice, skated in alone on Tuukka Rask and slid it past him for what turned out to be the game-winner.
Andrew Ladd got Winnipeg's other goal as the Jets handed the Bruins their first regulation-time loss in 16 games while moving above .500 (12-11-4) for the first time this season.
Rask ended with 33 saves for the Bruins.
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