The Greek club have been punished for crowd incidents ahead of their 2-0 loss against Ajax on November 27, when a section of AEK supporters threw a petrol bomb and flares into the stands housing Ajax fans.
They have also been ordered to pay a £70,000 fine and to play the next two UEFA competition matches behind closed doors.
In a statement released on Friday morning, the club had apologised for the behaviour of its own supporters and stated they will be taking action against fans should they create more trouble.
AEK Athens were knocked out of the Champions League group stages after suffering six defeats out of six games against Bayern Munich, Ajax and Benfica
They currently sit third in the Greek Super League behind leaders PAOK and rivals Olympiakos.