The Roar stormed back from going a goal down with a late, late double from Besart Berisha. The Albanian's second came with virtually the last kick of the game from the spot after he was awarded a penalty with a fresh air shot.
Even after the game, both Berisha and Roar teammate Matt Nichols admitted the penalty wasn't there - much to the frustration of Glory's players and their 2,000-strong away support.
''I don't have words really,'' Perth captain Jacob Burns said. ``You've got to congratulate Brisbane but I feel as though I've been robbed there. That decision cost us the grand final.''
It is the second year in succession that the Roar have come back from the brink to win the final - in 2011 they were 2-0 down deep into extra time before beating Central Coast on penalties.
''This team never dies,'' Brisbane captain Matt Smith said. ''No matter what the circumstances have been over the past two years we've never given up.''