Both clubs were charged on Friday by Football Federation Australia not only for the behaviour of their supporters but also for the dispute that erupted afterwards and had until January 7 to explain why they should not face sanctions, the FFA said.
"Football Federation Australia has announced that Melbourne Victory and Western Sydney Wanderers have been charged with bringing the game into disrepute by way of the misconduct of their supporters ...in Melbourne," an FFA statement said.
"Further, FFA has advised the clubs that their public statements this week on the events of 28 December are regarded as inappropriate and damaging to the interests of the ... A-League."
Local media reported a fight had broken out between opposing fans outside a bar in central Melbourne before their clash on December 28, which resulted in eight supporters needing medical treatment.
Western Sydney said Victory fans had sparked the fight while the Victory then said that flares had been set off by visiting fans inside the stadium during the match as both sides engaged in a public tit-for-tat blame game earlier this week.
FFA chief executive David Gallop has said both clubs could be docked three competition points at the end of the regular season, pending the further behaviour of their fans.
Any repeat of fan misbehaviour would incur the points loss and additional penalties, Gallop said.
"The loss of points that have been won fairly on the pitch is a harsh penalty, but it's in equal measure to the enormous damage caused by the type of anti-social behaviour seen in Melbourne last Saturday," said Gallop.
"The troublemakers are hurting the club they claim to support. They need to understand that the consequences of their reckless conduct will be felt on the A-League competition table if trouble persists."
Both clubs acknowledged the FFA's stance and said they were reviewing the decision before formulating a response.
"Western Sydney Wanderers FC reaffirms its position that anti-social behaviour has no place in our stands, in our game or in society," Wanderers said.
"The club fully supports all appropriate necessary measures to remove this minority element from our game.
"Any individual identified committing acts of anti-social behaviour, as evidenced today, puts themselves and the Club at risk of significant and heavy penalty."
Melbourne added they were seeking further advice from the A-League on operational procedures for the Wanderers' return match on January 14.
"Melbourne Victory in no way condones or tolerates the actions of a small minority that participate in anti-social behaviour in and around football matches, and has worked tirelessly with all stakeholders to identify and prosecute those responsible," the club said in a statement.
"The club, however, has requested and is still awaiting an operational plan from FFA on the revised match day arrangements for the return of the Western Sydney Wanderers on January 14."
The A-League has been relatively free from any fan violence since it began in 2005 after the previous national club competition was disbanded due to a multitude of issues, including several instances of fighting and hooliganism among fans of clubs that were drawn principally along ethnic lines.
Supporters of rival football codes have often used the threat of football violence, both domestically and overseas, to promote their own sports and keep the world's most popular game battling for profile and commercial opportunities in the crowded Australian sporting landscape.