The game took place in Larnaca in Cyrprus, with riot police being rquired to step in after clashes between stewards and fans of the Scottish side.
As a result, Aberdeen have been charge for 'crowd disturbances' and for having 'no stewards travelling with supporters', something which is against UEFA's safety and security regulations.
Apollon meanwhile were charged with 'setting off fireworks', 'throwing objects' and 'improper conduct of the team'.
The referee threatened to abandon the game after flares were launched towards 'Dons' goalkeeper Joe Lewis, whilst Aberdeen manager Derek McInnes vocal in his criticism of the treatment of the travelling fans.
McInnes said after the game: "I heard the stewards were very heavy-handed, going in with tear gas and being very aggressive.
"When supporters behind the dugout are spitting at our players, myself and the staff that is when stewards need to be more visible."
UEFA will deal with the case on August 17.