Adam Lowry counted the game winner 7:39 into the third.
Mark Scheifele and Mason Appleton had a goal and assist each for the Jets, who took 5 of 6 points in their three-game set this week.
Paul Stastny also scored for Winnipeg, who moved to 17-8-2 on the season and to within four points of the Maple Leafs for first place in the Northern Division, with two games in hand.
Laurent Brossoit stopped 20 shots for the Jets.
William Nylander and Jake Muzzin scored for Toronto, who dropped to 19-8-2 and remain winless in regulation in their last five contests.
Frederik Andersen stopped 27 shots for the Maple Leafs.
Toronto travels to Ottawa tomorrow to face the Senators while Winnipeg returns home to host the Canadiens on Monday.