The Roar's Melbourne Victory-bound striker Besart Berisha left it until the 85th minute to equalise, sending the match into extra-time.
And they finally put the anxious Roar faithful - and coach Mike Mulvey - out of their misery when Brazilian Henrique fired in the matchwinner in the 108th minute.
Then again Brisbane have never done things by halves in grand finals.
They won their maiden 2011 title by fighting back from 2-0 down in extra-time to down Central Coast on penalties.
And the Roar claimed the 2012 crown with a late penalty after reeling in a 1-0 deficit against Perth Glory.
It seemed a fitting end to a season Brisbane dominated, claiming the Premiers Plate by finishing 10 points clear of the Wanderers.
But A-League upstarts Western Sydney will be hoping for third time lucky after losing their second straight grand final in as many years of existence.
It seemed only something extraordinary was going to silence the relentless chants of the Wanderers' 10,000-strong Red and Black Bloc supporter group that effortlessly drowned out the local orange army.
But Brisbane's man for the big occasion - Berisha - did his best.
The Albanian international had tried in vain to get the Roar supporter group The Den involved by screaming at them to find their voice.
However, he didn't have to do much to pump them up when he equalised with a sublimely timed header off a Thomas Broich free kick.
And they had plenty more to cheer about as super sub Henrique pounced on James Donachie's cross to blast away at point blank range.
It capped a remarkable rise for Mulvey who emerged from obscurity to be installed interim coach with Brisbane in disarray in December 2012.
Mulvey had watched the Roar claim their first title from the grandstand as a punter.
Now Mulvey holds the reins of the A-League's most successful club after becoming just the fourth mentor to complete the minor premiership-championship double in a season.
Western Sydney at least had little time to wallow in defeat.
They fly out to Sydney on Sunday night to prepare for Wednesday's Asian Champions League match against Sanfrecce Hiroshima in Japan.
-AAP