Lokomotiv Moscow midfielder Dmitri Tarasov's vest showed Mr Putin in a navy cap along with the words "the most polite president".
The politically-charged Europa League match was the biggest sporting encounter between the nations since Turkey shot down a Russian jet in November.
Turkish side Fenerbahce won 2-0.
Lokomotiv Moscow are now likely to face punishment because European football's governing body Uefa does not allow political statements during matches.
But Tarasov later defended his behaviour.
"It's my president. I respect him and decided to show that I'm always with him and prepared to give my support," he told Russian news agency R-Sport. Read more on bbc.