The game was their lone visit to Winnipeg this season.
Ilya Sorokin made 24 saves for New York, who moved to 5-2-2.
Eric Comrie turned aside 29 shots for Winnipeg, who dropped to 6-3-2.
The loss was the Jets' first at home this season.
Anders Lee got the Islanders on the board 3:12 into the game when Josh Bailey outmuscled Adam Lowry behind the goal and hit Lee with a backhand pass.
Lee, who was alone in front of the Winnipeg goal, made no mistake firing a low shot past Comrie to give the Islanders a 1-0 lead.
The goal was his 2nd of the season.
There was no scoring in the second period.
Brock Nelson scored 47 seconds into the third to give the Islanders a 2-0 lead after taking a relay pass at the Jet blue line and moving in before firing a wrister, beating Comrie just inside the left post.
The goal was his 7th of the season and 5th in his last two outings.
Jets Head Coach Paul Maurice elected to pull his goaltender with 2:29 remaining to give his team a two-man advantage but the Jets were unable to score.
The Islanders visit Minnesota Sunday night while Winnipeg hosts St. Louis on Tuesday.
SHOTS-NEW YORK 31 WINNIPEG 24