In front of a sell-out 50,000-plus home crowd, Brisbane somehow managed to fight back from 2-0 down in the final minutes of extra time to draw 2-2 and take the season to a penalty shootout.
Two saves from goalkeeper Michael Theoklitos helped the Roar take the advantage with Henrique netting to clinch the championship 4-2 on penalties.
Earlier, after the score had finished 0-0 at 90 minutes, the Mariners appeared to have the title sewn up thanks to Adam Kwasnik and Oliver Bozanic both netting in extra time.
But somehow Brisbane fought back, with efforts from Henrique and Erik Paartalu to send the match into a shootout.
Paartalu, a free transfer from Greenock Morton last year, scored with the final touch of the game when he headed in from a corner on 120 minutes to send the game to penalties.