Berisha will move to Victory as their international marquee for the next two seasons, making the move as the most lethal striker in the A-League's history with 41 goals in just 65 appearances since joining Brisbane before the 2011-12 campaign.
Victory head coach Kevin Muscat claimed he cannot wait to work with a player who has given him plenty of headaches as a coach.
"Besart has been performing at the highest level week-in, week-out for Brisbane and has caused plenty of headaches for opposition defenders and coaches, including myself," Muscat said in a statement.
"He's a proven goal-scorer and a player that we can't wait to welcome to Melbourne Victory.
"It's certainly well documented how competitive Besart is and that is something every A-League fan surely admires about him."
Brisbane lobbied Football Federation Australia (FFA) last week for special dispensation to pay Berisha outside the salary cap next season as the 28-year-old Albanian was reportedly asking for a pay rise.
With Thomas Broich and Matt McKay already filling the Roar's two marquee positions, FFA's rejection of Brisbane's proposal put Berisha's future at Suncorp Stadium in serious doubt.
"With the salary cap we have in this league, the ins and outs of players are a fact of life," Brisbane head coach Mike Mulvey said.
The signing of Berisha indicates Chilean defender Pablo Contreras is unlikely to remain at the Victory next season, as the 35-year-old currently the club's international marquee slot.
