Edson Montano believed he had scored a second goal for Newcastle in the 31st minute after tapping in on the goal line.
Yet the assitant referee was flagging for offside and the offical disallowed the strike, despite Montano standing metres behind the ball when Andrew Hoole crossed in.
The contest began promisingly for Newcastle as Hoole burst into the box, but dragged his effort wide of the far post.
A youthful Western Sydney side responded on on the quarter hour as a Jaushua Sotirio shot hit the post.
On 21 minutes however Newcastle stunned the home fans.
Montano turned and found Enver Alivodic on the edge of the area. Ante Covic came a long way off his line to stop the Serbian.
Alivodic coolly dragged the ball wide of the goalkeeper and then fired into an open net to give the Jets a 1-0 lead.
Newcastle thought it had scored a second just past the half hour after Hoole got the better of his opponent, before his tame cross went straight through a Wanderers defender and fell perfectly for Montano, who tapped in from the goal line.
But it was inexplicably ruled out for offside, with replays confirming no such infringement.
Newcastle did score the second goal it deserved before the break.
Hoole played the ball into the path of the overlapping Lee Ki-Jee in the box. From an acute angle the Korean defender fired his shot into the top corner to make it 2-0.
Western Sydney hit back five minutes into the second half with a superbly curled free-kick from Nick Kalmar reducing the deficit to 2-1.
The Jets hung on for the three points which lifted them off the bottom of the table.
The two-time A-League grand-finalist and Asian champion remains bottom with its hellish schedule continuing to take a toll.
With injuries wreaking havoc on the Wanderers' squad, Popovic was forced to dig deep and field a line-up which featured seven players who've had less than 10 starts to their name.
"We didn't come into this game today thinking we couldn't win but the circumstances are what they are," Popovic said.
"We don't want to come last, certainly not. We're used to success here.
"We don't want the wooden spoon. That is obviously something that's in the back of the mind," Jets coach Phil Stubbins admitted.
"If you look at those amount of games where we've been accountable, to finally get a win down here is a great tonic for the group."
"Overall we started (the Newcastle game) bright but I think for them it would have been great if we took the lead, they would have relaxed a lot earlier.
"Then we made two very bad errors to give the goals away. It's the story of our season, we're always chasing the game and it was a lot of pressure for the young players."
