Key pair Joe Lolley and Corey Hollman joined Douglas Costa on the Sky Blues' injury list in a hectic defeat at Go Media Stadium.
Sydney centre-back Hayden Matthews appeared to have scored his first A-League Men goal in the 83rd minute to give the Sky Blues a crucial away win.
But after a lengthy VAR review, the goal was contentiously chalked off for offside, seemingly by Patryk Klimala in the build-up.
In the 97th minute, Jake Brimmer whipped in a free kick and Auckland centre-back Nando Pijnaker headed the ball to ground then backheeled it over the line.
97th minute. Backheel. Nando Pijnaker, TAKE A BOW �— Isuzu UTE A-League (@aleaguemen) The big centre-back scores a last-gasp winner to make it two wins from two for @fc_auckland.And the scenes are seriously special 💙🖤 pic.twitter.com/N7S1p6fe3eOctober 27, 2024
Former Sydney boss Steve Corica's Auckland held on to ensure a second win from as many games for the expansion club.
"It was an amazing match," skipper Hiroki Sakai told Sky Sports.
"It's also incredible, because we joined the A-League this year, but now we are top of the table. So this is a miracle."
Sydney coach Ufuk Talay was understandably fuming after the disallowed goal while he will also have to consider his mounting injury list.
Costa didn't play Sunday's game  after he was substituted with hamstring tightness in Wednesday night's 2-1 Asian Champions League Two away loss to Japanese club Sanfrecce Hiroshima.
On Sunday, Lolley was assisted from the pitch after just 35 minutes with an apparent groin injury and replaced by Patrick Wood.
Hollman had treatment on his ankle in the first half and made way early in the second.
Auckland should have taken the lead when Felipe Gallegos brilliantly slipped through Liam Gillian in the 55th minute, but he inexplicably lifted the ball onto the crossbar.
Sydney were screaming for a penalty when Francis de Vries appeared to drag down Klimala inside the box in the 59th minute.
But strangely, neither referee Shaun Evans nor the VAR intervened.
Jordan Courtney-Perkins forced a brilliant save from Alex Paulsen just before Matthews' would-be goal.
Then, Auckland failed to clear their lines multiple times and Matthews turned Anas Ouahim's driving ball home.
The goal was belatedly chalked off.
"They didn't really show the replay, so it was sort of hard to see," skipper Rhyan Grant told Sky Sports.Â
"But from the still shot I saw, I thought it was earlier in the play, but obviously it's offside.
"But yeah, it's a tough one to take."
Then Pijnaker delivered Sydney's undoing.
Auckland travel to take on Wellington Phoenix in their first derby on Saturday while Sydney are away to Brisbane Roar on Friday.
