The incident, which has been heavily criticized online, appears to have been fueled by Vitaliy Buyalsky’s celebration after he took the visitors 1-0 in the second half.
He also stated that it would be “unfair” to attribute this rhetoric to all fans.
Videos posted online show a large section of fans singing Putin’s name shortly after Buyalsky celebrated in front of home fans.
It came moments after Fenerbahce midfielder Ismail Yuksek was sent off in a heated match.
Vasily Bodnar, Ukraine’s ambassador to Ankara, said it was “sad” to hear the chants.
“It is very sad to hear the words of support from the Fenerbahce fans in favor of the Russian killer and attacker who is bombing our country.
“I am grateful to compatriots from Turkey for their support of Ukraine and for their attention to the inappropriate actions of fans.”
CNN has reached out to Dynamo Kyiv for comment.