Russia invaded Ukraine in February and the war has caused thousands of deaths while millions more have been displaced.
The chanting started after Oleksandr Karavayev scored what ended up being the winner for the Ukrainian side in the tie's second leg in Istanbul as it ran out a 2-1 victor on aggregate.
It led to Dynamo boss Mircea Lucescu boycotting the post-match news conference, and UEFA has now sanctioned the Turkish club for the behaviour of its fans.
The club has been fined €50,000, while a partial closure of at least 5000 seats has been ordered for Fenerbahce's next European home game for "the throwing of objects and transmitting a provocative message of an offensive nature, i.e. illicit chants".