With their lone goal coming off the head of Auckland defender Callan Elliot, it took until the 74th minute on Friday night for Alfie McCalmont to register the hosts' first shot on target on a sodden and sparsely attended evening in Gosford, and his effort only arrived after Auckland had taken a 2-1 lead.
Though unable to stretch early dominance across the full 90 minutes, the Kiwi side rarely looked troubled in easing to the win, striking first through Jesse Randall in the 20th minute, then securing their match-winning lead off Sam Cosgrove's head just before the hour mark.
Starting a run of fixtures where they will play six of seven on the road, Steve Corica's side moved two points clear of Sydney with the result.
The Sky Blues need to beat Perth Glory in Western Australia on Saturday if they wish to reclaim the summit.
With Francis De Vries twice picking out Cosgrove for headed attempts, Auckland could have put the contest to bed early if not for the heroics of Andrew Redmayne in the Mariners' goal.
However, the former Socceroo could do little when De Vries found space and slipped an inch-perfect, outside-of-the-boot pass for Randall with ample time to bury his effort.
Elliot inadvertently powered his attempt to head clear a Storm Roux cross into his own net in the 33rd minute, giving the hosts hope despite the Mariners failing to have a single shot in the opening half.
But just as they started to show more signs of life in the second half, Lachlan Brook found Cosgrove for a diving header and the lead.
In a further blow for the Mariners, late substitute Arthur De Lima pulled up lame with an apparent hamstring injury just moments after coming on.
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