Brisbane's win was tainted by the sending off of their star striker, who became the first A-League player to receive three red cards in one season when he was given his marching orders in the 49th minute.
The Heart, who paid tribute to the newly crowned A-League Premiers by giving them a guard of honour as they took the field, took a first-half lead thanks to a delightful team goal finished off by Aziz Behich before Dimitri Petratos equalised before the break.
A curling Henrique effort in the 73rd minute won the game for Brisbane after the Brazilian had come on as a substitute six minutes earlier.
Berisha was left in tears after being shown the red card four minutes after half-time as a result of lunging in for the ball at the same time as Heart goalkeeper Tando Velaphi and catching him in the head with his studs.
As it was only his second direct dismissal of the campaign, he will only receive an automatic one-match suspension, meaning he could be back for the Roar's final regular-season game.
