Ecuadorian striker Edson Montano's second half strike gave Phil Stubbins's side a deserved three points as it stunned the title favourite in its own backyard to leapfrog Western Sydney Wanderers and move into ninth spot.
Victory, which wasted the chance to move a step closer the Premiers' Plate, stays on top of the table, a point ahead of Adelaide United and level with Perth Glory, which can finish no higher than seventh as punishment for its salary cap breaches.
It was the Jets who created the first opening but Montano took the wrong option as he latched onto a Nick Cowburn cross, trying to cushion the ball rather than let fly.
Victory was quickly into its stride at the other end with Carl Valeri denied by a smart save from Jets keeper Ben Kennedy in the eighth minute after he had been released by Fahid Ben Khalfallah.
Playing with a freedom befitting a side with nothing to play for - other than avoiding the wooden spoon - the Jets sprung forward at every opportunity as Mitch Cooper blazed over in the 11th minute much to Victory's relief.
Victory found it hard to make headway against a determined and dogged opponent.
But veteran striker Archie Thompson did break the shackles to fire just wide in the 38th minute.
It was the Jets, though, who wasted two glorious openings inside 60 seconds before half time.
First, an unmarked Enver Alivodic headed wide of a gaping goal from Andrew Hoole's 42nd minute cross when it looked easier to score and then a stretching Cooper fired over after being set up by Alivodic.
The Jets did, however, take a deserved 54th minute lead when Alivodic cut down the right, rounded Daniel Georgievski, and crossed in the box where Nick Ansell fluffed his attempted clearance and Montano was on hand to poke home his fourth goal of the season past stand-in keper Lawrence Thomas.
Substitute Kosta Barbarouses squandered the chance to level matters in the 85th minute as he dragged his shot across the face of goal when well placed.
After the Jets had icked up a second successive away win, a delighted Stubbins said: “Did we believe that we could come to Melbourne and win? Yes, of course we did.
"We set ourselves up to win every game, and we prepared very well for this match. It’s a credit to everyone involved that we’ve come to AAMI Park and stamped our mark on the game.
"The win wasn’t a fluke, we had great periods throughout the match and importantly managed to keep a clean sheet which is a credit to everyone involved.”
"We made some tough decisions through this year which has led to us now having a rather youthful squad. What we have now is a young and vibrant team champing at the bit to represent Newcastle."
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