The naked body of the man with various injuries, including to his genitalia, was found in the courtyard of an apartment building May 10.
The victim's skull was smashed with a 20-kg rock and he appeared to have been raped with beer bottles. The suspects also tried to burn the body but failed to do so.
"The motive for the crime was the (victim's) non-traditional sexual orientation," said senior regional investigator Andrei Gapchenko.
Two suspected attackers have been arrested and another man is a witness in the case, he said.
The suspects are a 22-year-old man, who studied with the victim at school, and his 27-year-old friend, who was previously jailed for theft. The latter has admitted his guilt, investigators said.
This is a rare attribution by Russian law enforcement authorities of homophobia as a motive.
Gay activists claim information citing homophobia as a motive often disappears from investigation documents and such killings are investigated simply as domestic crimes.
A murder investigation has been launched. If convicted, the attackers face up to 15 years in jail.