Sydney FC stars Matt Simon and David Carney were also hit with yellow cards.
The drama appeared to blow up when one of the Victory officials was spotted by Fox Sports cameras striking Carney on the back of the head as he ran past the Sky Blues midfielder to celebrate with Melbourne players inside the penalty area.
With more than eight minutes remaining in extra time he was of course not allowed to be anywhere near the middle of the pitch.
The scuffle took the shine of Antonis' goal and has set a dramatic storyline to dominate the A-League's grand final week heading into the Victory-Jets decider in Newcastle.
Despite an outcry from commentators on social media, Victory coach Kevin Muscat suggested his coaching assistants should not be banned from appearing on the sidelines in the grand final.
When asked if he regretted the actions of his assistants, Muscat said he would have to look at the vision before passing any judgment on the ugly scenes.
"Look, I don't know. I haven's seen it played back," Muscat told Fox Sports.
"We'll obviously find out exactly what went on and we'll deal with it internally. What I will say is that it is an emotional game.
"Sensitivity is not something that is a strong suit if you want to be involved in something like football. There was a lot of passion and a lot of emotion and it would be disappointing... I hope common sense prevails. Whatever happened, they were punished tonight. Hopefully, next week, they'll be able to join us in the big dance."
Where Muscat was uncertain, commentators were damning of the black eye de Marigny and Anastasiadis have given the game.
It was only one of many moments of absurd drama during the crazy 120 minutes.
Prodigal son Terry Antonis propelled Melbourne Victory to an unlikely A-League grand final, scoring a stunning extra-time winner to defeat Sydney FC 3-2 and scupper the reigning champions' quest for back-to-back titles.
Victory reigned in a hugely antagonistic semi-final that ended with the dismissal of Victory's goalkeeper coach Dean Anastasiadis and assistant coach Jean-Paul de Marigny.
But the result will be remembered for the dreadful mistake and swift atonement of Antonis.
The former Sky Blue was close to tears when, with Victory up 2-1 and 13 seconds away from booking a spot in the decider, he netted a 95th-minute own-goal to hand his former team the 2-2 equaliser they'd so desperately craved. But, in the 117th minute, Antonis pounced on a turnover and blazed forward from halfway to fire the ultimate winner past a despairing Andrew Redmayne. His moment was overshadowed by farcical scenes when de Marigny and Anastasiadis were handed red cards for celebrating Antonis' goal in the face of their Big Blue rivals, the latter appearing to take a swipe at David Carney's face.
Nevertheless, there was no more stunning way for Kevin Muscat's men to snap their seven-match losing streak against the reigning champions, overcoming the burden of history and the untimely loss of Rhys Williams to inflict the premiers' first finals loss at Allianz Stadium.
The result is a massive blow to Sydney's two-year dominance and stops Graham Arnold going out on a high before taking over the Socceroos. Victory will play Newcastle next Saturday at McDonald Jones Stadium for their fourth title. The Jets will have watched in glee as their opponents pushed themselves past the point of fatigue for 120 minutes.
Victory were up against it from the moment Williams injured his quad in the warm-up and matters worsened when the defender's replacement Stefan Nigro buried an unfortunate own-goal to put the Sky Blues ahead early.
But the excellent Kosta Barbarouses pounced quickly for the first-half equaliser, before a moment of Besart Berisha brilliance allowed James Troisi to bury the would-be winner on 47 minutes.
Sydney forcing extra-time on the back of two own-goals was as inexplicable as it was shattering for a Victory side so close to snapping their Big Blue hoodoo. It followed an indescribable five minutes of injury time when young substitute Ben Warland rattled the crossbar and flicked another shot centimetres wide. Then, deep into added time, a mad scramble in the box ended with Adrian Mierzejewski cutting back from the byline towards Antonis, who will long regret swatting his attempted clearance straight into his own net.
The ball splayed out of Lawrence Thomas' reach, which was even crueller, given the goalkeeper's repeated heroics to keep his side on track for a win that had seemed so doubtful but eventually came.
