The game appeared to be headng for a goalless draw before referee Lucien Laverdure ruled that former Wanderers defender Daniel Mullen had handled in the box - and substitute Brendan Santalab stepped up to bury the 85th minute spot-kick.
But debutant Lee Ki-je delivered a stoppage leveller for Phil Stubbins' men as they grabbed a deserved draw to keep their noses in front of the rock bottom Wanderers in front of a crowd of 11,019.
The Korean showed nerves of steele to plant home the game's second penalty after Antony Golec had been penalised for handball in the 92nd minute after Nick Cowburn's goal-bound effort had struck him.
The draw was a much-needed boost for Newcastle, who conceded an own goal last week in injury time to lose 2-1 to Brisbane after a fortnight of turmoil.
Five players and three staff were sacked by Jets owner Nathan Tinkler, who has been issued a show-cause notice by Football Federation Australia over his management of the embattled club.
The result was a further blow for the Wanderers, who created the bulk of chances in the Round 17 match.
Stubbins praised his weakened and young side's effort to scrounge out a draw with the Asian club champion and said it was reward for the group remaining positive despite the recent upheaval.
"I'm extremely happy for the group," Stubbins said. "Obviously Tony [Popovic] has got a terrific team there on paper, a great team on paper, so for us to come back like we did, certainly with the youth we had on the pitch, is fantastic for everybody.
"I think it's an indication to the supporters that we're trying to get people on board who want to play in the right way for us in terms of having a crack.
"Then to score the goal at the end like we did, the group was fantastic to do that. It's a credit to them that they came back and found a way to get a result."
The Wanderers remain without an away win in eight attempts this season.
"Second half we certainly dominated and should have been up by two or three goals before we got the penalty," said coach Tony Popovic.
"In the end, unfortunately, we couldn't see it out. We were so close to getting that first win today and second half was a dominant display, we deserved that.
"But when you are not up by two or three, the ball can bounce around and things can happen, so we've got to be a bit more ruthless in putting teams away when we have the opportunities."
The first half belonged to the Wanderers, with the Jets' goal leading a charmed life at times.
Socceroos defender Matthew Spiranovic should have done better when an error from Jets keeper Ben Kennedy resulted in him being presented with a gaping goal early on, but he fired wide from just outside the six yard box.
Labinot Haliti thought he had given Western Sydney a 35th minute lead with a crisp finish, but his effort was ruled out for offside.
Four minutes later Tomi Juric was denied by a tip-away save from Kennedy as the Socceroos marksman turned away from his defender and burst menacingly into the box to fire off a left-footed drive.
Skipper Taylor Regan should have given Newcastle the lead in the 53rd minute with its first real chance only to head centimetres over when unmarked from Andrew Hoole's inswinging corner.
It was the signal for the Jets to lift the tempo as it poured forward in waves before appearing to run out of steam.
Laverdure denied Nikolai Topor-Stanley a tap-in finish after whistling for a foul on Kennedy before the game exploded into life in the dying minutes.
