It was a rare moment of goalmouth quality in a match which had sadly lacked it, but the previous 88 minutes were made worthwhile when Brandon O'Neill's superb pass was sumptuously controlled by Ninkovic, who then arrowed a shot past Andrew Redmayne into the bottom corner.
The game may have been even, but this was a flash of quality which deserved to separate the two teams on the night.
The atmosphere at Allianz Stadium was raucous and the early tackling matched it.
O'Neill's crunching tackle on Scott Jamieson in the centre of the park set the tone for a first half that was largely bogged down in similar sorts of confrontations.
Ninkovic nearly lit up the opening exchanges with a shot that skewed ever-so-slightly wide, before Wanderers returned serve when Romeo Castelen's cross narrowly missed the late-arriving Jaushua Sotirio.
Unfortunately for Castelen his night was ended early when he picked up a hamstring injury only ten minutes in. He was replaced by Dario Vidosic, but for the neutrals it was a shame for Castelen would have been a treat to watch once the game had settled into its groove.
Dimas's blushes were spared when he hit the crossbar from almost underneath it, but he was deemed correctly to have been offside when Vidosic at the back post nodded a Jamieson cross back into the area.
The warfare continued in the centre of the park when Dimas smashed Ninkovic and became the first name in the referee's notebook. Dimitrijevic joined him when his lunging tackle caught Sotirio.
In the middle of all this, some football broke out, when Rhyan Grant, playing again out of position at left back, bombed forward. His one-two with Alex Brosuqe was delightful, but his finish was not, as he blazed it into the RBB behind Andrew Redmayne's goal.
Wanderers thought they'd taken the lead in stoppage time when Sotirio's header from a Nicholls cross looped over Vedran Janjetovic, but Sotirio was marginally offside.
Neville should have seen a second yellow when he took out Ninkovic. The proof was in the pudding, for he was substituted immediately after, replaced by Brendan Hamill.
Graham Arnold replied in turn, injecting Andrew Hoole and Mickael Tavares into the action, in place of the anonymous Filip Holosko, and Dimitrijevic.
There was definitely more football being played, but chances were still at a premium. Federico Piovaccari nearly connected with a Sotirio cross, before he was bundled over moments later by Jacques Faty, who was booked for his troubles.
Jamieson whipped a cross/shot in from the resulting set piece that sailed over the bar, much to the delight of the sky blue crowd. It summed up the goalmouth action thus far.
The excellent Matthew Jurman had to be alert to stop Piovaccari shooting after a lovely turn, and the crowd began agitating for a goal.
Janjetovic nearly took matters into his own hands when he flapped at a long ball forward under pressure from Piovaccari, evoking memories of his nightmare own goal at the same ground last season.
Substitute Matt Simon had a late chance for Sydney FC but didn't connect cleanly with a header.
All was forgotten though, when Ninkovic showed all his class and quality to fire Sydney FC to the sweetest of victories.
Sydney FC 1 (Ninkovic 88')
Western Sydney Wanderers 0
Western Sydney Wanderers 0
Allianz Stadium, Sydney
Referee: Ben Williams
Crowd: 40,539
Referee: Ben Williams
Crowd: 40,539
