The fine was accompanied by a warning over the lack of stewards travelling with Dons fans.
The club were charged over crowd disturbances after riot police moved in following the third qualifying round match on August 3 when travelling fans clashed with stewards.
UEFA's disciplinary body also fined Apollon 27,500 euros (Â£25,000) for fireworks and "throwing of objects" charges, along with the improper conduct of the team after they received five yellow cards during their 2-0 second-leg win, which saw them progress 3-2 on aggregate.
Flares were lit early in the second half in the home section of the AEK Arena in Larnaca, with one thrown and landing inside the goal behind Aberdeen goalkeeper Joe Lewis.
Television pictures caught Swiss referee Stephan Klossner telling an official that he would abandon the match if the behaviour did not cease.
Source : PA