The result makes A-League history as Brisbane become the first team to win three Championships, with their run interrupted by the Central Coast’s title last year.
The match was a typically tight Grand Final to start, with Western Sydney starting to take the momentum in the early going, having the first chance in the 22nd minute.
Jerome Polenz was given space and made a good run down the wing and sent in a cross for Brendan Santalab but the striker just couldn’t get his head to the ball, allowing Brisbane to clear.
In the 27th minute Brisbane had their first chance of the match as Thomas Broich was allowed to turn and shoot but sent his effort just wide.
Right before half time the Wanderers could well have had the opener as Iacopo La Rocca sent a ball back, trying to find Youssouf Hersi but he couldn’t find the striker, letting Brisbane off the hook.
An Ivan Franjic cross nearly paid off for Brisbane late in the half as his effort came off of the cross bar before Ante Covic held on to Luke Brattan’s effort, to keep it scoreless at the break.
Western Sydney came out from the break the better side as they forced Brisbane back with Shinji Ono forcing Brisbane to scramble a ball clear in the early going.
In the 56th minute the opener did finally come as Matthew Spiranovic beat Broich and ran in to head home Ono’s corner, scoring the club’s first ever Grand Final goal.
Disaster struck for the Wanderers in the 72nd minute as Nikolai Topor-Stanley challenged Besart Berisha and injured himself, forcing him to be replaced.
Chasing the match, Brisbane went for the match, needing a goal to get back in to the match but the Western Sydney defense was much too strong.
Broich sent in a ball for Berisha with a perfect through-ball, allowing the Albanian to run in to the box, but was denied as Spiranovic came down and lunged out to deflect the shot out.
Broich continued to link up well with Berisha and found him with a free-kick but he sent his effort wide of goal.
The German veteran then tried to go on his own as he forced Henrique off balance but couldn’t find the target as he sent his effort over the bar.
Hersi had a golden opportunity in the 84th minute as Tomi Juric crossed in for Hersi but he sent his effort wide of goal.
Just two minutes later Brisbane were back on level terms as Broich and Berisha linked up well again as Broich sent in a free-kick for Berisha who headed it home for the equalizer with time running out.
Both sides tried to have chances late on but neither could put a chance away as the Grand Final went on to extra-time.
There was plenty of space at the back in the extra-time periods as both sides struggled with their tired legs but the tired legs were struggling for finishing for the same reason.
Labinot Haliti had a solid chance in the early stages as he cut inside Jade North but saw his effort saved by Michael Theo.
After half-time in extra time Brisbane started to dictate terms and in the 108th minute they had their goal as Henrique was left wide open the penalty area as the ball found the Brazilian who stabbed the ball home to seal the win and the trophy.
Drama seems to be par for the course when it comes to Hyundai A-League Grand Finals at Suncorp Stadium and the latest instalment continued the tradition with Brazilian forward Henrique smashing in a goal in extra time to give the Brisbane Roar a 2-1 comeback win over the Western Sydney Wanderers.
The Roar have now won three out of the last four A-League titles to stake a strong claim to be the finest side in the short history of the competition.
The Wanderers, meanwhile, have reached two Grand Finals in the two-year life of the club, only to lose them both.
A tight contest was generally expected in the build up to the match, and the two teams delivered.
A tense opening half was followed by a more flowing second term, with the Wanderers' captain Matthew Spiranovic finding the net after 56 minutes only for the Roar to find an equaliser through Besart Berisha who, in his last game for the club, scored from a Thomas Broich assist.
It was the visitors who settled into the game sooner, but Brisbane dealt comfortably with a series of early Western Sydney corners and free kicks delivered into the box.
An advancing Jerome Polenz galloped into space down the right after 22 minutes, then sent a dangerous cross in for Brendon Santalab, who could not quite stretch far enough to turn it in.
The first genuine chance of the half came in the 27th minute, when Thomas Broich received the ball with his back to goal, turned, and fired a stinging low shot just wide of the upright.
The Wanderers came very close to breaking the deadlock just before the break when Iacopo La Rocca cut a ball back inside the area which just failed to find the feet of a lurking Youssouf Hersi.
It was Brisbane who finished the half the stronger, however, with Ivan Franjic thumping the woodwork with what appeared to be a cross from wide on the right, and Luke Brattan trying a shot from a tight angle on the left that was gathered by Ante Covic.
The Wanderers once again came out of the blocks quicker in the second term, with Hersi and Shinji Ono combining well in the Brisbane area only for the defence to scramble the ball clear.
Chances also fell to Berisha and Franjic as the game opened up.
It was the Wanderers who broke through with the opening goal from a set piece four minutes before the hour mark when Spiranovic lost Broich, his marker, to angle home Ono's corner with a powerful header.
Six minutes later, Western Sydney lost their captain to injury, as Nikolai Topor-Stanley twisted his knee when making a desperate challenge on Berisha.
Brisbane stormed forward following the goal, with Broich in particular threatening to unlock the Wanderers' defence.
A sublime through ball from the German found Berisha in the box, and the striker weaved inside before firing an effort on target, only to be denied by a heroic lunge from Spiranovic which deflected the shot wide.
A free kick from Broich again found the Albanian, but his header was well off target from close range.
Broich then came close himself from distance, before substitute Henrique was off balance when he scooped a shot over the bar from inside the box.
Another visionary pass from Broich landed at the feet of Franjic on the right of the Wanderers' box, and the defender cut inside and blasted a shot towards the near post which Covic palmed away brilliantly.
Hersi nearly doubled the Wanderers' advantage but was unable to scramble in a Tomi Juric cross, and the visitors would be left to rue the miss two minutes later.
Broich and Berisha finally got their combination right with four minutes of regular time remaing, with the forward slipping between two defenders to head in the German's curled free kick.
There was time for chances at both ends before the 90 minutes was up, but nobody could break the deadlock and the match went to extra time.
Tired legs ensured there were plenty of gaps for attacking players to exploit once extra time got underway, with Franjic and Hersi getting away attempts on goal at either end.
It was then Haliti's turn to try his luck. The substitute flew down the left, jinked inside Jade North and sent a firm shot at Theo, who was able to parry.
The Roar were dictating play overall as extra time wore on, and Henrique eventually broke through with the decisive goal after 108 minutes.
The Brazilian was loitering near the penalty spot when a low pass from the right found him somehow alone in a crowded area, and he blasted the ball into the centre of the net to sound the crowd into raptures.
Brisbane Roar 2 (Berisha 86', Henrique 108')
Western Sydney Wanderers 1 (Spiranovic 56')
Crowd: 51,153 @Suncorp Stadium