The UEFA charges facing AEK include a pitch invasion by their fans, the throwing of objects, setting off of fireworks, insufficient organisation and the display of an illicit banner.
Ajax have been charged with setting off fireworks and the throwing of objects by their supporters.
The governing body's Control, Ethics and Disciplinary Body will deal with the case on Dec. 13.
Former European champions Ajax beat AEK 2-0 to reach the knockout rounds of the continent's elite club competition, while AEK were eliminated from Europe after a fifth straight defeat.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
(Reporting by Simon Jennings in Bengaluru; Editing by Ken Ferris)
