With the Victory third and the Japanese side last in Group F, both sides desperately chased victory in an entertaining affair at AAMI Park on Tuesday night.
It was Barbarouses who finally found the back of the net in the 90th minute to seal a breathtaking win in front of 6639 fans.
With two matches left in the group stage, the win puts the Victory right in the hunt to progress to the round of 16.
But in what is sure to be a major talking point, Victory striker Besart Berisha was furious at being substituted in the 70th minute, storming past Kevin Muscat to take his place on the bench.
The Victory were all at sea in the face of an impressive opening onslaught by the visitors.
The crisp ball movement of the reigning J-League champions opened up the home side time and again, with Kei Chinen unlucky not to convert one of two gilt-edged scoring opportunities.
Yoshito Okubo's searing strike from just outside the penalty area 10 minutes in forced a brilliant save from Lawrence Thomas, who tipped the ball onto the crossbar.
But having absorbed the opening blows, the Victory warmed into the contest and were unlucky not to go ahead in the 20th minute.
The ball spilled to James Troisi on the edge of the box after Kawasaki keeper Jung Sung-Ryong slipped over while attempting to clear an ill-advised back pass.
But Troisi's deft shot was cleared off the line by Sung-Ryong's quick-thinking teammate.
Thomas was called into action again when he somehow managed to gather Okubo's shot from point-blank range before the Victory's Thomas Deng drove a shot over the bar.
It was end-to-end stuff after the restart as both teams redoubled their efforts.
Substitute Yu Kobayashi's header found the back of the net, but was flagged offside, with the Victory denied by the post soon after.
The match appeared headed for a draw before Barbarouses found himself in the right spot and stroked the ball home between the keeper and the post.