The incident, which was heavily criticized online, appeared to be sparked by Vitaliy Buyalskyi’s celebration after he put the visitors 1-0 up in the second half.
It also said it was “unfair” to attribute the rhetoric to all its fans.
Videos shared online appear to show a large section of fans singing Putin’s name shortly after Buyalskyi had celebrated in front of the home fans.
It came moments after Fenerbahce midfielder Ismail Yuksek was sent off in a fiery match.
Vasyl Bodnar, Ukrainian Ambassador to Ankara, said it was “sad” to hear the chants.
“It is very sad to hear the supporting words of the Fenerbahce fans — in favor of the Russian murderer and assaulter who is bombing our country.
“I am grateful to fellow Turkish people for their support to Ukraine and for their consideration about the inappropriate actions of the fans.”
CNN has reached out to Dynamo Kyiv for comment.