Football Australia has promised to investigate and hand down "strong sanctions" after Melbourne City goalkeeper Tom Glover was left with a cut head and a suspected concussion.
Glover was struck by a metal bucket when fans from the Melbourne Victory active area stormed the pitch.
Referee Alex King was also injured, suffering a head gash in the same incident, shortly after the 20-minute mark of Saturday night's game at AAMI Park.
Both sets of fans had been throwing flares onto the playing arena.
But the situation escalated when a flare hit a Network 10 cameraman, then exploded when Glover picked up another flare off the ground and threw it back into the stands.
Fans then rushed the pitch and Glover and King were both struck by the metal bucket, which is filled with sand and used to dispose of flares.
Glover immediately started bleeding from his temple and needed medical assistance.
An FA spokesperson confirmed King, who had put himself between Glover and the fans, was more rattled than hurt.
The referee match-day coach was pushed into the fence and security later escorted all officials to their cars.
FA has promised heavy penalties.
"Such behaviour has no place in Australian Football, with a full Football Australia investigation to commence immediately, where strong sanctions to be handed down," a Football Australia statement said.
After the incident involving Glover and King, players from both teams were rushed down the tunnel, while fans were swinging from the goal at the Victory end of the ground.
The game was paused before officials made the decision to abandon the fixture.
City players later returned to the pitch to thank the fans but Socceroos winger Mathew Leckie had a bottle thrown at him when he headed back down the tunnel.
There had been a tense atmosphere early in the match with both sets of active fans planning to leave the game at the 20-minute mark as part of a protest towards the Australian Professional Leagues.
Fans across the competition were protesting the league's decision to sell the next three grand finals to Sydney.
Both sets of fans started "f*** the APL" chants immediately after the preceding A-League Women's game finished.
Victory and City fans each unfurled banners pre-game and during the match, referencing their displeasure with the APL.
Victory fans let off small fireworks then flares, while their goalkeeper Paul Izzo had to help dispose of flares thrown by City fans.
The game then descended into chaos.
City led 1-0 when the game stopped, courtesy of Aiden O'Neill's goal in the 11th minute.
