The Albanian striker was shown a straight red when he dived for a ball and his boot caught goalkeeper Tando Velaphi in the head.
Berisha had just returned from a one-match suspension after being sent off in the match against Sydney FC in Round 23, and he becomes the first player to receive three red cards in a single A-League season.
As they have done on previous occasions this year, Brisbane dominated the match despite being a man down, with substitute Henrique scoring the winning goal in the 73rd minute.
The Roar's top scorer is due to serve another one-game ban, though his manager was confident the red card would be rescinded, a scenario which is unlikely to occur under Football Federation rules.
"I think it was the wrong decision," said Mulvey.
"Bes has seen his chance, he's lunged for the ball, he's made contact with the ball, he's at full stretch, what's he supposed to do? Seriously?"
"I'd be having a go at him if he didn't go for it because that's the chance of a goal."
Mulvey hinted that the firey forward's reputation often landed him in trouble with referees, even if he wasn't necessarily in the wrong.
"It's like flavour of the month at the moment; there's Bes, let's give him a red card," he said.
"He's feeling like the whole world's against him at the moment.
"We'll appeal this.
"In fact I don't think we'll even need to appeal it, because I think they'll have a look at it and say this is not the right decision."
Berisha himself was left sobbing on the turf after referee Chris Beath brandished the red card, but he can take some consolation from the fact his teammates seem to lift every time he receives his marching orders.
