In an enthralling grand final at Suncorp Stadium, Brisbane equalised in the 86th minute through Besart Berisha before going on to seal a third crown in four years.
Matthew Spiranovic had headed the Wanderers ahead from a corner 11 minutes after half-time, yet Tony Popovic's men were ultimately denied as Brisbane benefited from another dose of late drama.
Henrique was on target three years ago when the Roar came from two down in extra time before beating Central Coast Mariners on penalties, while the team's 2012 success came courtesy of a controversial late penalty from Berisha.
On this occasion, the pivotal moment arrived in the 108th minute as Henrique rose to flick on a cross from the left before remaining alert to gather the ball from James Donachie and fire home a powerful shot on the turn.
Defeat was harsh on Western Sydney, who looked set to avenge last year's final defeat to the Mariners courtesy of Spiranovic's opener.
The Australian defender lost his marker before angling home a powerful near-post header from Shinji Ono's right-wing corner.
Yet Brisbane refused to give in and claimed a late leveller when Berisha, playing his final game for the club before his move to Melbourne Victory, capitalised on similarly slack defending at the other end to convert Thomas Broich's free-kick.
Substitute Labinot Haliti had a golden chance to put the Wanderers back ahead seven minutes into extra time, but failed to beat Michael Theo in the Brisbane goal.
And it was to be the hosts who grabbed a crucial second as Henrique once again rose to the occasion.
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