Frank Farina's struggling Sky Blues were searching for only their second win in eight games at the expense of the current league leaders, and they achieved it thanks to Emerton's 89th-minute strike.
Central Coast striker Daniel McBreen had a good chance to put his side ahead in the first half but Vedren Janjetovic palmed his angled shot to safety and then Sydney began to pile on the pressure with Rhyan Grant hitting the crossbar five minutes from full-time.
Former Blackburn midfielder Emerton was then in the right place to head home Alessandro Del Piero's late cross and the Mariners soon self-destructed.
Skipper Josh Hutchinson was dismissed for a reckless lunge, before Tom Rogic followed him down the tunnel for a two-footed tackle, as the visitors lost for the first time since October.
Sydney climb above Melbourne Heart - who lost at Wellington Phoenix - and into ninth place with Central Coast missing the chance to extend their two-point lead over Adelaide United.
Wellington had earlier fought back from two goals down to register the 3-2 win that moved them into sixth place.
Melbourne's Golgol Mebrahtu got the ball rolling in the 14th minute to make it 1-0, with defender Andrew Durante making life even harder for the hosts with an own goal just two minutes later.
Louis Fenton's response in the 21st minute ensured Wellington had a fighting chance going into the break, though, and Jeremy Brockie would complete the turnaround on his own in the second half.
The New Zealand international drew the Phoenix level from the penalty spot in the 66th minute before firing the winner four minutes later.
Elsewhere, Perth Glory and Western Sydney Wanderers shared a 1-1 draw that stabilises both sides' chances of booking a final series play-off place.
Labinot Haliti gave Wanderers the lead in the 38th minute but Nick Ward hit back three minutes from full-time to ensure the points were shared.
Western Sydney rise one place to third, while Perth Glory remain in fifth spot, two points clear of Wellington.