The red card given to the Phoenix defender Ryan Lowry on Sunday night will stand.
Lowry was sent of after 75 minutes in the 1-1 draw with the Perth Glory in Wellington.
The referee originally gave a direct free kick to Perth for a tackle by Lowry, but the video official intervened as it was felt contact by Lowry with his studs to Chris Okonomidis' leg met the considerations for serious foul play.
The Referees Department's weekly post-round review decided that the correct outcome should have been a yellow card for a reckless tackle.
However the red card was upheld as the Match Review Panel can only overturn a red card if all 3 panel members determine that in the circumstances no card was warranted.
Lowry gets an automatic one-match ban and will miss this weekend's game against Sydney.
The Phoenix coach Mark Rudan got stuck into referee Adam Kersey at the after-game media conference.
Rudan sais he believed time should be called on the VAR system and then saved his best for Football Federation Australia, who he accused of treating the Wellington club differently because of their historic struggles and the fact their existence is a source of contention.
"Little old Wellington Phoenix. I spoke about this when I first came to this football club, that nothing goes our way," Rudan said.
"Everything goes against us because no one wants us around. And here we are six weeks into the season and we're seeing this happen."
Rudan said his players were devastated, having been on course to topple the league leaders following Roy Krishna's club record 34th goal put them deservedly in front.
It prompted his call for a "civil discussion" with all stakeholders to assess the merits of the VAR system.
"It's become a bit of a mockery," he said.
There is no news yet on any possible sanction for Rudan following his comments.