Guillermo May was the hero for the Black Knights, with the substitute equalising twice in the 67th and 90th minutes in front of 16,661 fans at Allianz Stadium on Sunday.
Ben Garuccio's 55th-minute strike had given the Sky Blues hope of leapfrogging Auckland on the table in their final home-and-away match, as had Alexandar Popovic's 85th minute strike to restore Sydney's lead.
Given five minutes of added time, Auckland couldn't find the match-winner to lock up a top-two finish, while Sydney also missed the chance to improve their finishing position.
Auckland (42 points) can finish runners-up and earn a weekend bye heading into the finals behind premiers Newcastle (48) if Melbourne City (38) keep Adelaide United at bay (40) later on Sunday.
Black Knights coach Steve Corica is resigned to their fate.
"It's up to Adelaide now," Corica said.
"A little frustrated, but obviously a tough place to come here as well.
"All in all, probably pleased with the point in the end."
Sydney (39), led by interim coach Patrick Kisnorbo, had to win by at least three goals for a chance to finish second.
The Sky Blues have now been winless in all six matches - including an Australia Cup clash - against Auckland.
Kisnorbo's fifth game at the helm since replacing Ufuk Talay will be an elimination final.
"There's a lot of talk, talk, talk, but the main focus is what we do inside here and how we go about it," Kisnorbo said.
"That's the only thing you can control, that's the main thing. Whatever happens after that really is irrelevant."
A week off before a two-legged semi-final will come in handy for Auckland, who were forced to add midfielder Felipe Gallegos to their injury list.
The Chilean midfielder, who has played 23 matches this season, went down with a suspected left hamstring issue in the 22nd minute.
Auckland boss Steve Corica is also hoping to regain defender Frances De Vries (calf), with midfielder Jake Brimmer (calf) and centre-back Nando Pijanker (shoulder) also on ice.
Sydney's best chance at a first-half opener came in the 35th minute, when Garuccio cleverly worked his way through the opposition defence only to be denied by the post.
Tiago Quintal backed up Garuccio's effort seconds later and forced a save out of Auckland goalkeeper Michael Woud.
The visitors managed just two shots before halftime, with English forward Sam Cosgrove unable to add to his league-best haul of 11 goals.
Cosgrove at least becomes the first international player to win the golden boot since Wellington's Fijian striker Roy Krishna scored 18 goals in 2018/19.
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