Wanderers were minutes away from winning the Grand Final through a Matthew Spiranovic strike 11 minutes into the second half.
However, Besart Berisha, playing his last game for the Roar, marked his final appearance in fairytale fashion by equalising on 86 minutes, before Henrique pounced with the clincher midway through extra time to seal the triumph.
Sydney, who were beaten finalists last year, made inroads toward banishing the memories of the 2012-13 campaign by taking the lead on 56 minutes through Spiranovic, who rose highest from a corner to thump his side into a one-goal advantage.
It was not enough to gain victory, though, as Berisha - who has scored 31 times in 39 games at the Suncorp this season - maintained his stellar goalscoring record in timely fashion to head home the equaliser and force extra time.
The game beckoned for a hero throughout the additional half hour as Labinot Haliti went close for Sydney, but Henrique rifled a shot into the roof of the net shortly after the break to claim Brisbane's third A-League title.