Riot-trained police dispensed tear gas to chase away the dozens of angry fans who ran onto the pitch and destroyed advertising signs, while a number of flares were also thrown by supporters.
Two hours before the match about 100 Olympiakos hooligans fought briefly with police outside the Karaiskakis Stadium and a window was smashed on the coach carrying the AEK players after it was pelted with rocks.
Olympiakos will likely face punishment from the league following the trouble, with a heavy fine and possibly a deduction of points.
AEK won the match in dramatic fashion through a 94th-minute goal by forward Giorgos Giakoumakis, after Ukraine defender Dmytro Chygrynskiy had cancelled out a strike from Olympiakos's Karim Ansarifard with just three minutes left.
The victory moved AEK into second place with 44 points, two points behind league leaders PAOK Thessaloniki. Defending champions Olympiakos dropped to third place on 42 points.
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