The league's disciplinary committee handed down the punishment on Friday after Panathinaikos's derby match against Olympiakos Piraeus at the Olympic Stadium last Saturday was abandoned after being interrupted twice by crowd trouble.
The league said the match would be recorded as a 3-0 loss for Panathinaikos who would also pay a fine of 252,500 euro for failing to maintain order at the game.
The club were deducted three points from this season and two points from the 2012/13 season.
The strict penalties are part of a new sports law which the Greek government passed in February aiming to clamp down on football violence.
Panathinaikos have exercised their right to appeal and their case will be heard next week.
The violence at the Olympic Stadium, the ground which hosted the 2004 Olympics, was some of the worst seen in recent seasons.
The start of the second half was delayed by 45 minutes as fans pelted police with Molotov cocktails, flares and missiles, and the game was subsequently abandoned altogether with nine minutes remaining with Olympiakos 1-0 ahead.
Twenty police officers were injured and more than 50 arrests were made while three fire engines were called in to extinguish flames as hundreds of fans set alight sections of the stands. Three of those arrested were charged with possession of explosives, police said.
The club had already been in trouble with the Super League's disciplinary committee this season for crowd violence and were forced to play one match behind closed doors earlier this month.
With five games remaining, Olympiakos now have an 10-point advantage and look odds-on to retain their Super League title, which would be their 39th.
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