The league's disciplinary committee also fined the Greek champions €90,000 for the pitch invasion on February 4, during which hundreds of fans fought running battles with riot police and flares were thrown onto the pitch.
The points deduction is a major blow to Olympiakos' title ambitions.
The Piraeus club, who are likely to appeal against the decision, are in third place and now have 40 points, nine points adrift of leaders PAOK Salonika after 21 games.
The players had to rush off the pitch at the Georgios Karaiskakis stadium as irate Olympiakos fans broke through security and ran onto the pitch where they fought with police.
During the match a flare had also exploded at the feet of AEK players on the pitch.
The Super League punishment mirrors similar decisions taken against Panathinaikos and PAOK last term, with the authorities taking a sterner line in recent years due to state legislation passed by the government to crack down on crowd violence. REUTERS
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