Newcastle Jets seemed set for a perfect start under new coach Scott Miller until the Glory's Sidnei Sciola equalised with a close-range header three minutes from the end to push the game into extra time.
And the visiting Perth took the lead for the first time just two minutes after the restart in Broadmeadow as Nebojsa Marinkovic, who set up Sciola's goal, coolly netted from the penalty spot.
Newcastle had earlier taken a first-half lead through a typically sweet David Carney strike, with the former Socceroo playing his first match since January after being exiled from the squad under former coach Phil Stubbins.
The Jets also had a Labinot Haliti goal chalked off for a controversial offside. However, Haliti eventually got on the scoresheet drawing the Jets level in the dying minutes of extra time to force penalties where Glory goalkeeper Jerrad Tyson made three saves to help last year's cup finalists advance.
At Penrith in western Sydney the Wanderers overcame a slow first half showing to prevail against Brisbane.
Golgol Mebrahtu netted the only goal of the game with 20 minutes remaining, and Mark Bridge could have extended the winning margin but his late penalty was saved by Roar goalkeeper Jamie Young.
The final match of the evening saw Melbourne-based Oakleigh Cannons edge out Far North Queensland 5-4 on penalties, following a 1-1 draw.
Jamie Gosling equalised with a speculative long-range effort in the final minute for the Queenslanders after Jamie Piemonte had scored with a stunning strike early during extra time.
-AAP