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Former Burnley striker Besart Berisha scored the only goal of the game in the second half to send Roar, who finished top of the regular season table, through to the playoff showdown for the third time in four years.
Luke Brattan quickly got Brisbane on the front foot and twice nearly gave them the lead inside the opening five minutes, firstly with a free kick that drifted wide and soon after with a back-heel.
Archie Thompson tested Roar keeper Michael Theo with a powerful shot on 10 minutes, while Berisha worked Nathan Coe at the other end before the break, and was also played in by ex-Manchester United midfielder Liam Miller, only to be flagged offside towards the end of what was an even first half.
Berisha got another sight of goal early in the second period and took it, squeezing the ball through Coe at the near post having created the chance himself with a mazy run which took him past two defenders.
Roar had chances to extend their lead but had to endure a nervy finish on a one goal cushion, with Theo called upon to deny Thompson and Melbourne skipper Mark Milligan as Brisbane nervously hung on.