City goalkeeper Tom Glover was left bloodied after being struck in the face by a metal bucket as Victory fans stormed the Melbourne Rectangular Stadium pitch, resulting in the abandonment of the match.
In addition to the fine, the club was handed a suspended 10-point deduction which will automatically be triggered by each and every incident of "serious supporter misconduct" over the remainder of this and the subsequent three seasons.
Victory have also been banned from selling tickets for the area of the ground from which the fans invaded the pitch and will not receive any allocated seating at away matches for the rest of the season.
FA calculated that these sanctions would cost the club another A$100,000 (€65,000).
The match will be replayed in April starting from the 22nd minute with City retaining the 1-0 lead they held when the fans invaded the pitch.
FA chief executive James Johnson said the scenes were the "worst" the Australian game has seen since the start of the A-League era in 2004.
"The field of play is sacred and the safety of our players and match officials is paramount," he said in a statement.
"Those individuals that illegally entered the field of play, caused damage, and verbally and physically assaulted players and officials, crossed the line.
"The sanctions imposed on Melbourne Victory are a necessary step to ensure we create an environment where we place football first, and our community can enjoy matches."
FA have already handed out bans, some for life, to 17 fans identified as having been involved in the incident.
Victory later released a statement saying the club would not appeal the punishments.
"Melbourne Victory will comply with all sanctions handed down by FA in its final determination and is working with the relevant stakeholders to ensure its matches moving forward will be a safe environment for players, fans and everyone involved," it read.