Ruslan Sokolovsky, 22, pleaded not guilty to the offence in a court in the city of Yekaterinburg.
The prosecution called for him to be sent to a penal colony for 32 months, but instead he was given a three and a half year suspended sentence.
Sokolovsky was arrested in 2016, shortly after uploading the video of himself playing the game on his smartphone.
The footage has been viewed almsot 2m times on YouTube.
It was filmed inside the Church of All Saints in Yekaterinburg - a Russian Orthodox church built on the spot Tsar Nicholas II and his family were killed in 1918.
In the video he ridiculed legal warnings against playing such games in churches.
"Who can ever be offended by you walking around a church with your smartphone?" he asks before entering the church and saying it was not prohibited by law.
On Thursday, he was found guilty of insulting religious believers and inciting hatred, as well as of "illegal trafficking of special technical equipment" when a pen with a hidden camera was discovered in his home.
Judge Yekaterina Shoponyak found Sokolovsky guilty of the same offence for which members of a controversial feminist punk band were jailed in 2012.
Judge Shoponyak had earlier stated that Sokolovsky's video and behaviour had displayed a "disrespect for society" and that he had "intended to offend religious sentiments".