Friday's appearance in Moscow began with Elton, settled behind a black grand piano, reading a monologue in which he called for harmony and inclusion for all.
"You've always embraced me and you have never judged me," the composer said in reference to a long line of visits to Moscow that began with a groundbreaking concert in 1979.
That Soviet-era performance transformed him into a household name -- an impact still felt in Russia to this day.
Elton was careful not to criticise either Putin or his supporters directly for fast-tracking controversial legislation.
But neither did he hide his disappointment.
"I am deeply saddened and shocked over the current legislation that is now in place against the homosexual community here in Russia," he said to a scattering of applause.
"In my opinion, it is inhumane and it is isolating. Harmony is what makes a happy family and a strong society."
Elton concluded the speech by dedicating his concert to Vladislav Tornovoi -- a 23-year-old Russian whose naked body was dumped in the city of Volgograd after he had been raped with beer bottles and had his skull smashed.
A witness told the police at the time of the May attack that Tornovoi was targeted for being gay.