Roar have now captured their second consecutive A-League Championship.
Glory led from the 51st minute to the 84th, before the competition's top scorer Besart Berisha headed the equaliser with six minutes to go.
Just like the 2011 edition, the match appeared set for extra-time, only for referee Jarred Gillett to award the home side a penalty in the final seconds of injury time.
Berisha slalomed his way into the Glory penalty box and appeared to be tripped while taking a shot on goal.
The Perth players remonstrated furiously, with replays showing no contact had been made on the Albanian frontman.
But they were powerless to stop Berisha hammering home the spot-kick to claim a brace and win the match in dramatic and controversial fashion.
Glory had been on the cusp of an historic win after taking the lead when a cross deflected off Ivan Franjic for an own goal in the 51st minute.
Billy Mehmet was the architect, splitting the Roar open with a scything run through the midfield.
He delivered to the right flank where Travis Dodd skidded through a low cross which ricocheted off Franjic and into the back of the net.
Brisbane probed and pushed relentlessly in chase of their equaliser, and in the end it was produced by the likely suspects, with A-League Player of the Year Thomas Broich sending in the perfect cross for Golden Boot winner Berisha to head past a helpless Danny Vukovic.
Dean Heffernan then left the visitors a man down for the final seconds, after taking out Franjic in injury time to collect his second yellow card, having earned his first for a needless challenge on Broich.