They also have been charged over bunch disturbances after flares threw into the stands housing Ajax fans, with pictures showing flames burning area.
Ajax are charged with projecting objects and setting off fireworks.
December, the situation will be dealt with by UEFA on Thursday.
AEK happen to be sanctioned for a total of seven incidents such as:
- Crowd disturbances
- Throwing of things
- Placing from fireworks
- Field invasion by fans
- Lack organisation
- Displaying illicit banner
- Blocking stairways
As firecrackers were set off at the start of the second half there were crowd disturbance and players from either side could be seen rubbing their eyes as smoke drifted across the Athens Olympic Stadium.
Images also showed police officers hitting on on Ajax fans, leaving a few with blood pouring down their faces, while Ajax defender Matthijs de Ligt ran over to the fans to plead for calm.
The Eredivisie side secured victory through two goals from former Southampton forwards Dusan Tadic to progress to the last 16 for the first time since 2005.
AEK, who had Marko Livaja are bottom of Group E without any points.