The Dons face two disciplinary charges over “crowd disturbances” and “no stewards travelling with supporters”, the latter in contravention of UEFA’s safety and security regulations.
The Cypriot team face three charges - “setting off of fireworks”, “throwing of objects” and “improper conduct of the team”.
Riot police moved into the away section of the AEK Arena in Larnaca as Aberdeen fans clashed with stewards after last Thursday’s 2-0 defeat saw their team go out 3-2 on aggregate.
Flares were lit early in the second half in the home section, with one thrown and landing inside the goal behind Aberdeen keeper Joe Lewis. Television caught Swiss referee Stephan Klossner telling an official that he would abandon the match if the behaviour did not cease.
Speaking about the incident after the game, Aberdeen boss Derek McInnes told BBC Radio Scotland: “It is ridiculous behaviour, that we have to deal with that. It didn’t help the flow of the game in the second half but I don’t think he (Lewis) was damaged, I don’t think it affected him too much.
“We expected it to be a wee bit volatile and plenty of passion from the side but it did boil over at times.
“I am hearing our fans got treated terribly as well by the stewards here, steaming in with flares and tear gas and everything else to defuse the situation.
“I didn’t get to see it but I am hearing it second hand and you seen some of the stuff that was going on, things getting thrown on to the pitch, people spitting into the dugout, flares getting thrown on - that’s when you should have seen the stewards being more visible, not treating our fans the way they did.”
Aberdeen later announced they had begun an investigation into the fighting in the away section.
Apollon automatically triggered the improper conduct charge after receiving five yellow cards.
UEFA’s disciplinary body will deal with the case on August 17.