Melbourne Victory were "disappointed" by the sanctions but accepted responsibility for the way a "marginal element" behaved during the derby clash with Melbourne City.
FFA stated that the punishment was not only for flares but for, "an alleged assault on TV news personnel outside the stadium, throwing missiles at a Melbourne City player and a Victoria Police officer, and altercations with police after the match."
Victory coach Kevin Muscat hailed the club's supporters and atmosphere at games but stressed fans cannot cross the line.
"I'm deflated. The behaviour is illegal. The live atmosphere at a Melbourne Victory game is unrivalled, but anti-social behaviour must stop," he said.
Melbourne Victory Chairman Anthony Di Pietro echoed Muscat's sentiments, issuing a plea to the fans to unite and stamp anti-social behaviour out of the game.
"We ask every Victory fan to unite. Our message is clear & simple - no more flares, no more anti-social behaviour. Enough is enough," Di Pietro said.
Muscat also opened the door for Australia striker Tim Cahill to join the A-League after departing Chinese Super League side Shanghai Shenhua.
"Timmy could raise the roof, he's got some decisions to make, he's welcome here," he said.