The 2-2 result sees Brisbane progress to the A-League grand final 4-2 on aggregate and the right to host it.
The Mariners shocked the strong home crowd with two goals in a minute late in the first-half. A Matt Smith own goal and Oliver Bozanic's rasper had the visitors 2-0 up at the break.
The Roar rallied midway through the second-half as German midfielder Thomas Broich forced his strike past Mariners goalkeeper Matt Ryan.
Brisbane sealed a home grand final when Brazilian substitute Henrique swept in to keep in tact his side's 27-game unbeaten record with a 90th-minute equaliser.
The Mariners will now host the winner of Adelaide United-Gold Coast United in the preliminary final next weekend.