Hundreds of fans invaded the pitch, throwing flares and fireworks and clashing with riot police, rival fans and even players, following AEK's 3-0 win over Atromitos at the Olympic Stadium on April 30.
The punishment from the Greek football federation's disciplinary committee, which included the largest fine it has handed out this season, means AEK will play their remaining two home matches in the Super League play-offs as well as the first competitive game of next season without fans.
Atromitos were also ordered to play two matches behind closed doors and fined 60,000 euros.
Last month, players' union chief Stelios Giannakopoulos said Greek football's image had been "smeared" and needed a major overhaul to rid itself of the crippling problem of crowd violence.
Violence inside and outside stadiums has plagued Greek football this season, endangering the safety of players and fans.
Leading clubs Olympiakos Piraeus, Panathinaikos and PAOK Salonika have been punished with supporter bans after ugly pitch invasions involving battles with police and attacks on players.
The Greek Football Federation (EPO) has been warned it will not receive "a single euro" of government money unless it can wipe out the unruly fan behaviour which has disrupted the domestic season.
The government have announced that a new sports bill will be drafted in June, which would enable authorities to hand out stricter penalties, while EPO are expected to announce sweeping changes to their disciplinary codes when its general assembly convenes early next month.
