Substitute Shane Smeltz, for the second successive week, was the Sky Blues' saviour as he struck late to put Graham Arnold's men ahead, with marquee striker Marc Janko netting the second of his brace in stoppage time to seal Sydney's first home win in seven matches.
Defender Rhyan Grant notched Sydney's other goal with a long-range belter in a gripping contest.
Fabio Ferreira replied with a double for Central Coast but, in the end, it wasn't enough in what was a much improved performance from Phil Moss's men.
After being rolled 5-1 by Sydney FC last time they met, the Mariners were out to settle the score but ultimately couldn't match the firepower of the Sky Blues' attack who have scored a massive 15 goals in their past four games.
After the disappointment of missing out on the AFC Asian Champions League with a limp 3-1 loss against Guangzhou R&F, the Mariners needed to make a statement and will take heart from the performance, if not the result.
The first clear cut chance fell to the Mariners when Isaka Cernak burst onto Nick Fitzgerald's raking long-range pass in the 10th minute but showed too much of the ball to keeper Vedran Janjetovic who smothered the danger.
But the Mariners were behind four minutes later when midfielder Milos Dimitrijevic sent over a pin-point corner which marquee striker Marc Janko headed emphatically past the hapless Liam Reddy for his ninth goal of the campaign.
The visitor almost hit back instantly, but Cernak lacked composure again and was denied by Janjetovic for the second time after being played in by Storm Roux.
Then new boy Fabio Ferreira cut the ball back for Fitzgerald, who slid his shot wide when he should have scored on the edge of the six-yard box.
At the other end, Reddy palmed away a trademark Dimitrijevic free-kick in a clash of end-to-end action.
The Mariners grabbed a deserved equaliser a minute into first half stoppage time when Ferreira latched onto Antony Caceres's defence splitting pass, skipped inside Jacques Faty and clipped his shot over the diving Janjetovic.
The Sky Blues keeper then thwarted Ferreira in a one-on-one situation after Nick Montgomery had carved the opening in the 53rd minute.
But there was no denying the former Adelaide United man five minutes later when he drilled a low shot past Janjetovic to put the visitor ahead after Cernak had splintered the Sydney defence with a jinking run and lay off.
But Sydney was level in the 68th minute when substitute Grant unleashed a swerving drive from 25 metres which gave Reddy no chance.
And the Mariners' hearts were broken in the 82nd minute when substitute Smeltz - who scored twice off the bench to rescue a point against Melbourne Victory last weekend - beat two defenders in the box after latching onto to a chestdown from Janko before planting the ball past Reddy for the clincher.
Janko side-footed home his second in stoppage time after young left-back Alex Gersbach had laid the ball on a platter for the Austrian for his sixth in four games and 10th of the season.
“We scored two great goals and we should have had another three or four comfortably so the main lesson we take from tonight is that we need to take our chances,” said disappointed Mariners boss Moss.
“I’m pinching myself after that. The best team lost on the day. We threatened every time we went forward, created something like 10 goal-scoring opportunities which is the type of football I want to play.
"I've said all along I want our football to excite our fans and I think Ferreira as an example was outstanding and he’s still not fit, when we get him 100 per cent match fit imagine what a player he can be."
His Sky Blues counterpart Arnold said: "Positive out of it is four goals and three points and the character we showed when we went down to comeback.
“I have to say the Mariners were good today and it’s very healthy when I can look down the bench and bring someone on like Shane Smeltz who can change the game.
"I’m happy with the result, and that puts us in good position now to move forward (ahead of next weekend's derby against Western Sydney)."
“I know that the fans have gone home extremely happy, the spectacle of six goals and the way we finished the game.”
