The match was played in unpredictable weather at a rain drenched Allianz Stadium on Saturday night.
The locals opened the scoring with Ninkovic burying an early opener in the fifth minute. The second goal in the 59th minute was a mastermind creation with quick passes towards the goal.
Newcastle Jets keeper Duncan releasing the slippery ball and directly moving it towards Bobo for a quick tap-in in the 59th minute allowed SydneyFC to extend the lead 2-0.
In the 65th minute, Sydney keeper Andrew Redmayne had made some early saves in both halves, but was outplayed by Newcastle Jets Petratos long range kick skidding off the greasy surface into the back of the net.
The victory has led to Sydney FC reclaiming top spot from the previously unbeaten Newcastle Jets FC.