Adelaide were up 3-2 on Saturday when Victory appealed for a penalty after Reds defender Panagiotis Kikianis slid in for the ball, appearing to get a touch to it, before collecting Daniel Arzani.
After a VAR review, referee Shaun Evans pointed to the spot, ruling Kikianis hadn't made contact with the ball.
Arzani converted the equalising penalty in the 71st minute, then red-hot Socceroo Nishan Velupillay orchestrated two goals in three minutes for matchwinner Nikos Vergos, who'd only come on as a late sub, in the dying moments at AAMI Park.
"It changed the momentum of the game," Veart said of the penalty award.
"I don't know what the messaging was between the VAR and the referee, but the decision was 'Pana' touched the ball and it was a corner, that's what he gave.
"You can clearly see on the video, on the TV, even live that he got a touch on the ball, and then he comes over, looks at it and says the reason for the penalty is he didn't touch the ball.
"If he didn't touch the ball, then yes, I agree it's a penalty - but he touches the ball. You can clearly see it in the video.
"So I just don't understand why he's called over to have a look at it to change his decision when there's clear contact on the ball.
"I'd like an explanation, because it doesn't matter after that. Why?"
When asked if Adelaide would seek an official explanation, Veart said: "Yeah we've already had contact.
"But officials always seem to back themselves.
"Have you ever seen them come out and say, 'yes, that was completely wrong'? They will always find an excuse."
Victory counterpart Arthur Diles said: "There's contact in the box and it's a penalty. It's pretty simple for me ... it's a clear pen and the game goes on."
Arzani told Paramount Plus: "I thought it was absurd that he didn't give it straight away, to be honest.
"He's just absolutely taken my legs out, he's maybe got a tiny snick on the ball but the ball's still in play for me to take and continue my run on ... obviously with VAR he (the referee) fixed it."
The result keeps the Victory in the race for a top-two spot with four games left while condemning Carl Veart's sixth-placed Reds to a six-game winless run and putting their finals hopes in peril.
The home side were without Ryan Teague (knock) and Adelaide opened the scoring in the 12th minute through a wonderful Jonny Yull strike.
Arzani equalised in the 29th minute and 10 minutes later, Velupillay put the Victory in front.
Adelaide equalised three minutes after halftime through Archie Goodwin, then Zach Clough restored their lead from the spot in the 56th minute.
After Arzani's equaliser, Velupillay danced through the area then found Josh Rawlins, who squared it for Vergos to tap home in the 88th minute, just three minutes after Diles had brought the Greek striker off the bench to replace Bruno Fornaroli.
Two minutes later, Velupillay brilliantly burst forward, then worked the ball for Vergos to sweep home the sealer.
Adelaide next host Sydney FC on April 5 while the Victory have the bye.