The Sky Blues and Wanderers were headed for a first goalless derby when O'Neill played in the gifted Serbian who lost defender Alberto with an exquisite first touch before finding the far corner of the net with a rifled shot that sealed an undeserved victory.
Ninkovic, who played for Serbia against Australia in the 2010 FIFA World Cup in Nelspruit, South Africa, was thrilled to be able to leave his mark on his first derby in the A-League.
But Ninkovic was quick to underline O'Neill's telling contribution to his winning goal - with the 21-year-old now having started all three games this season at the expense of experienced import Mickael Tavares.
"Brandon gave me a great ball and my first touch was good, which made it easy for me to score," Ninkovic, 30, said.
"Brandon is young but he's already a good player.
"If he continues to play like this I'm sure he will become a great player."
Ninkovic will not easily forget his first taste of Sydney's derby after his late heroics took the team to the top of the league and made him an instant hero among the Sky Blues fans.
"I was very happy because the goal came in the 88th minute so it was a very special moment for me," he said.
"This was my second game (in Australia) and I felt great although I must admit that I was not that satisfied with my performance.
"I just hope that I will get better with every game I play."
Ninkovic signed for the Sky Blues in the off-season from Evian in France after a distinguished career in the Ukraine and Serbia, where he played for the likes of Dynamo Kyiv and Red Star Belgrade.
"The football style is different to that in Europe but from the physical side the game here is like in France," he said.
Many players at all levels often point out that a derby is just another fixture but Ninkovic does not share that view.
"I don't think derbies are just another game," he said.
"Derbies are special games and if you win it feels like you have earned six points not just three.
"I thought the game would end 0-0. Western Sydney played really well tonight and controlled the ball and forced us to defend.
"It was a very big game, as derbies usually are. I don't think we played very well but the important thing is we got the three points.
"I have played in many big games in Europe such as the Belgrade derby between Partizan and Red Star and I can say that as far as I'm concerned this derby (atmosphere) is similar to the one in Serbia."
Ninkovic said he wished to dedicate the derby win to team-mate Ali Abbas, who is on the comeback trail after tearing his anterior cruciate ligament last season.
Abbas took part in the pre-game derby warm-up with the team and received a warm round of applause from Sky Blues fans when he left the field to head down the players' tunnel.
