The Super League's disciplinary committee dished out the punishment on Friday after AEK's match against fellow strugglers Panthrakikos at the Olympic Stadium last weekend was abandoned due to a hostile pitch invasion by home fans.
The league said the match would be recorded as a 3-0 loss for AEK, deducted three points from this season's tally and two from the next campaign, and slapped the club with fines totaling 4,000 euros.
The deduction leaves AEK five points from safety ahead of their final match against Atromitos on Sunday and if the decision remains unchanged after an appeal, one of Greece's biggest clubs will drop out of the top flight for the first time in their history.
In a statement published on the league's official website, the disciplinary committee said it accepted referee Stavros Tritsonis's match report which stated the inability to continue the match due to the "unusually catastrophic state of the pitch and surrounding area".
The league added that it found the club culpable because AEK had "failed to take appropriate measures for the safe conduct of the match and for the overall maintenance of order".
AEK called the decision a "pre-meditated crime by a corrupt system" in a strongly worded statement responding to the announcement and their intention to exercise their right to appeal, set to be heard next week.
"Today the disciplinary body of the Super League has decided to deprive us on paper of the right to fight for our salvation," AEK said.
"The corrupt system has found AEK guilty... This represents a pre-meditated crime with the perpetrators in principle Tritsonis and the disciplinary committee... and other instigators of a septic system."
The statement concluded: "AEK never gives up, however, because we have learned to play through on the pitch until the end. Starting on Sunday in Peristeri (against Atromitos) and then next week at the Court of Appeal where we believe we will be finally vindicated."
The strict penalty comes as a result of a sports law the Greek government passed in February 2012 aiming to clamp down on violence.
AEK are the second club to suffer from the application of the law after Panathinaikos received a similar points deduction punishment last year when a derby match against Olympiacos Piraeus was abandoned following a pitch invasion.
The violence at the Olympic Stadium, the ground which hosted the 2004 Olympics, was the latest low point in a turbulent season for the club.
Players from both teams were chased off the pitch by angry home fans after the hosts conceded an 87th-minute goal in the crucial relegation clash.
After a 90-minute delay, referee Tritsonis announced that the match was being abandoned.
AEK has been operating on a shoe-string budget following a period of financial turmoil in which virtually the entire first-team squad was sold off in order to secure a licence and preserve their top-flight status.
Club officials have been seeking new investors but after the recent collapse of a potential deal with London-based investment bank Seymour Pierce, their efforts have been unsuccessful.
The problems have not stopped there in what has been the worst campaign in club history.
Groups of supporters have staged regular protests at the training facilities due to the state of the team's finances, while the Nazi-salute goal celebration of midfielder Giorgos Katidis last month provided another blow to AEK's reputation.
Katidis was banned for five matches, fined 1,000 euros and also received a life ban from all national teams by the Greek Football Federation for making the gesture after scoring the winning goal in a 2-1 league victory over Veria.