A "technical failutre" with the VAR stopped the controversial technology from disallowing the goal that decided Saturday night's A-League grand final.
Kosta Barbarouses scored the only goal of the match in the ninth minute on Saturday to give Melbourne Victory a 1-0 victory over the Newcastle Jets and a record fourth Australian title.
The New Zealand winger's team mate James Donachie appeared to be in an offside position when he headed the ball back across the box from Leroy George's free-kick but, the FFA said, a 30 second blackout meant the VAR was unable to review the play.
"The technology itself failed and the broadcast angles required were unavailable," A-League chief Greg O'Rourke said in a statement.
"We are working with Hawkeye to thoroughly understand why it did and what can be done to prevent this happening again.
"We are extremely disappointed at this failure of the VAR technology and we understand the disappointment and frustration of the Newcastle Jets, their fans and indeed all football fans."
The Jets finished bottom of the league last season and were looking to complete a fairytale turnaround in front of a capacity crowd of 29,410 at their own stadium.
