The explosive 28-year-old, playing his last season for Roar before crossing to Victory, charged into the box in the 57th minute before blasting home between keeper Nathan Coe and the near post to sink his future employers.
"It's not an easy situation for me, but this is my job," Berisha said in a pitchside interview at Brisbane's Lang Park stadium.
"I have to finish to the last of my contract."
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Berisha's brilliant individual effort helped two-times champions Roar into their third final of the past four seasons, but the home side were also fortunate to escape without a late penalty when Victory skipper Mark Milligan was brought down in the box in injury time.
Victory coach Kevin Muscat stalked match officials as they walked off the pitch, barking his displeasure with the play-on decision.
"It's a bit difficult to take at the moment," he told host broadcaster Fox Sports, fuming.
"That's taken the biscuit. I'm also embarrassed ... It's a shame a decision by an official has dictated our season."
The Roar could also thank keeper Michael Theo for a string of fine saves in the final minutes as Victory pressed desperately for an equaliser.
In the same chaotic passage that saw Milligan go unrewarded, defender Matt McKay headed the ball off the line to stop a certain equaliser.
Victory's veteran striker Archie Thompson also tested Theo with a pair of long-range shots in the second half, prompting the keeper to remonstrate heatedly with his team mates for slackening off in defence.
Roar, who won the Premier's Plate, the trophy given to the team at the top of the standings at the end of the regular season, will host last year's finalists Western Sydney at the same stadium in a week as they bid to add to their back-to-back titles in 2010-11 and 2011-12.
In only their second season, the Wanderers will contest another final after defeating Central Coast Mariners, the team that beat them for last year's championship, 2-0 at home on Saturday.
Although playing away, the Tony Popovic-coached Wanderers fancy their chances of winning a maiden title next week and are riding a wave of confidence after booking a place in the knockout rounds of the Asian Champions League tournament earlier in the week.
"This time everyone is ready and available and the ACL I think has made us mentally tougher," Popovic said of his side, who belted China's Guizhou Renhe 5-0 on Tuesday.
"There's a real resilience about them now."
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