Jaushua Sotirio scored the 89th-minute winner to break a 2-2 deadlock that lasted more than an hour on Wednesday night and give the Wanderers their second win of the tournament.
In a frantic start, the hosts found themselves down 1-0 after just 21 seconds, before racing back to a 2-1 lead five minutes later.
It was a remarkable turnaround for Tony Popovic's men, who copped the third-fastest goal in ACL history when Wu Lei struck from just inside the area from the kick-off.
By the third minute Jumpei Kusukami had brought the hosts level, latching onto a Terry Antonis ball and firing home before the Japanese import set up Steven Lustica for the Wanderers' second in the sixth minute.
It sent the small Red and Black Bloc contingent into flare-ignited raptures at Campbelltown Stadium, where 5,271 had turned out for the dead-rubber match that doubled as a farewell to departing foundation player Shannon Cole.
Predictably, SIPG coach Andre Villas-Boas didn't risk his star Brazilians Oscar and Hulk given his Chinese Super League giants are already safely through to the knockout stages.
And with nothing on the line for either side, the contest was played with a jaunty freedom underpinned by brittle defence at both ends.
Perth-bound Scott Neville was a late pullout, leaving Jonathan Aspropotamitis to play out of position at right-back.
Aritz Borda plugged the gap in central defence, where he botched a tackle on Elkeson to concede a 23rd-minute penalty that the Brazilian striker duly converted.
A cagier second half allowed for few openings but Jumpei notched another assist late, SIPG's goalkeeper for Sotirioto prod home.