Ajax fans came under attack before kick off in the Greek capital as home supporters threw flares into the stands housing the Dutch supporters.
Photos showed police officers hitting Ajax fans, leaving some of them caked in blood in the away end.
Footage posted on social media also appeared to show a man leaving the AEK stands to throw a molotov cocktail at the Ajax supporters.
Ajax defender Matthijs De Ligt went over to the visiting fans and tried to calm the situation.
There were, though, further crowd disturbances during the second half, with several firecrackers being set off.
Members of both teams were seen to be rubbing their eyes as smoke drifted across the stadium.
Governing body UEFA will deal with the case on Thursday, December 13.
AEK face charges under article 16 of UEFA's disciplinary code, for the throwing of objects, the setting off of fireworks, a field invasion by supporters, crowd disturbances and displaying an illicit banner. The Greek club also have a case to answer over "insufficient organisation" and blocked stairways.
Ajax, meanwhile, have also been charged with the setting off of fireworks and the throwing of objects.
On Friday, November 23, both clubs were handed out sanction by UEFA following previous incidents.
After issues during the away match against Benfica, Ajax were handed a fine of 8,000 euros (£7,240) with a suspended sanction "for a probationary period of one year" of a ban from selling tickets to its away supporters. The Dutch club were also ordered to contact Benfica "for the settlement of the damages caused by its supporters."
AEK, meanwhile, had been fined 64,000 euros (£57,900) following problems at the game against Bayern Munich during October.
UEFA's Control, Ethics and Disciplinary Body also handed out a partial stadium closure sanction "where its ultra-supporters are situated", which was suspended for a 12-month probationary period.
Given the developments from Tuesday's matches, both clubs could now face those measures being implemented as well as any additional punishments from the governing body.
Ajax won the game in Athens 2-0 to secure progress through to the knockout stages of the Champions League for the first time since 2005.