One of the incidents for which the Turkish club have been punished involved a cat entering the field of play in the early stages of the second half in the last-16 tie.
The animal briefly brought play to a halt at the Vodafone Arena, before going on to win a man of the match poll held by the Bundesliga giants.
The incident has been described on UEFA's charge sheet as 'insufficient organisation', with Besiktas also disciplined for the 'throwing of objects' and 'stairways blocked'.
Bayern were also fined on Wednesday for a separate incident during their semi-final with Real Madrid – a human pitch invader and illicit banner leading to a €25,000 (£21,944) punishment.
Meanwhile, time-wasting by ball boys during Roma's clash with Shakhtar Donetsk earned the Serie A club a warning from UEFA, with the setting-off and throwing of fireworks incurring a €7,000 (£6,144) fine.