There were ugly scenes before kick-off in Athens as home fans were pictured throwing flares and other missiles into the away section of the Olympic Stadium, with some images showing flames erupting on the terrace.
Riot police were also seen striking Ajax fans, some of whom were left with bloodied faces.
Police had also faced trouble from a number of supporters in central Athens earlier in the day and on Monday evening.
Petrol bombs were also used during those disturbances, with traffic blocked before order was eventually restored.
UEFA confirmed on Wednesday that both clubs have been charged with throwing of objects and setting off of fireworks.
AEK also face charges of field invasion by supporters, crowd disturbances, insufficient organisation, displaying an illicit banner and blocking stairways.
The case will be heard by UEFA's Control, Ethics and Disciplinary Body on December 13.
Ajax claimed a 2-0 victory to book their place in the last 16 and leave AEK facing elimination from European competition this season.