Sky Blues defender Alex Popovic was set to be the unlikely hero, scoring his first goal for the club when he glanced in a header in the 84th minute of a hotly-contested game at Leichhardt Oval.
Sydney would have leapfrogged Auckland into second with victory on Tuesday but there was a late twist when Jordan Courtney-Perkins attempted to clear the ball out of his own box in the 95th minute.
The ball cannoned off teammate Alex Grant and into the back of Harrison Devenish-Meares' net as Auckland held on for a point.
Sydney sit third (26 points) and Auckland (29 points) are still second behind table-topping Newcastle (33 points).
It's the second game in a row that a late howler has led to Sydney dropping points, after Devenish-Meares made a crucial gaffe in last Saturday's loss to Adelaide.
"I'm deflated, but this is why we love the game so much," said Sydney coach Ufuk Talay.
"To capitalise late in the game and then to concede in the dying minutes brings you back down to earth. We definitely dropped two very valuable points at home.
"I think one thing in our change room is the boys know they played well."
Auckland coach Steve Corica remains undefeated in all his games against his former club and goalkeeper Michael Woud had a big part to play in that in the first half.
"It's obviously pleasing, but I would have liked the three points," Corica said.
Woud thwarted close-range efforts from Victor Campuzano when the Spaniard and Tiago Quintal were particularly threatening.
Auckland striker Sam Cosgrove escaped punishment for what appeared to be a stamp on Paul Okon Jr, while Sydney also had a strong case for a penalty turned down when Apostolos Stamatelopoulos was felled in the box by Jake Girdwood-Reich.
Cosgrove was eventually shown his fifth yellow card of the season, which will rule him out of Saturday's New Zealand derby against Wellington, with Corica then taking the striker off.
"We didn't want to go down to 10 men and we knew he was going to miss the next game," Corica said.
Talay threw Pierro Quispe on in the final 15 minutes in search of a match winner and the Peruvian looked to have delivered when he crossed for Popovic's late goal.
But in haste to clear their lines, Courtney-Perkins and Grant got in each other's way, with the ball firing back into Devenish-Meares' goal.
16°C