Home fans were pictured throwing flares and other missiles into the away section of the Olympic Stadium ahead of November's group game between the sides, which Ajax won 2-0.
Some images showed flames erupting on the terrace and riot police were also seen striking Ajax fans, some of whom were left with bloodied faces.
AEK were charged by UEFA following the game and the organisation's Control, Ethics and Disciplinary Body announced the Greek club's punishment on Friday.
A statement said: "The UEFA Control, Ethics and Disciplinary Body has decided: To exclude AEK Athens from participating in the next UEFA club competition for which it will otherwise qualify. This sanction is suspended for a probationary period of two years.
"To order the club to play its next two UEFA competition matches as host club behind closed doors. To fine AEK Athens €80,000."
Ajax were also charged by UEFA after the game but proceedings against the Dutch club have now been closed.
AEK are third in the Greek Super League after 21 rounds of games, sitting outside the Champions League qualification places.
"Our club apologised publicly and immediately, and recognised its part of responsibility about what happened," said a club statement in response to UEFA's punishment.
"The most important thing for all of us is to realise and think about that this decision does not mean the end of this incident, but the beginning of an extremely difficult road of complete compliance with the actual meaning of this decision, along with the need of taking drastic action in order to avoid finding ourselves at this position ever again, because in that case there will be no return!"