Vladimir Krasnov and Aleksei Stolyarov said they called the singer in a prank call, one impersonating the Russian president and the other posing as a translator, after John told reporters he wanted to meet Putin to discuss lesbian, gay, bisexual, and transsexual (LGBT) rights.
The gay singer posted a picture of Putin on his Instagram account thanking him for the conversation.
However, a Kremlin spokesman denied the Russian leader made the call.
“Pranks are funny. Homophobia, however is never funny,” John wrote on his Instagram account.
“I love Russia and my offer to talk to President Putin about LGBT rights still stands. I will always stand up for those that are being degraded and discriminated against.”
Western states and human rights activists have criticised Russia for its treatment of gay people. John has previously spoken out against a 2013 law banning the dissemination of “gay propaganda” among young people.
“If this unfortunate incident has helped push this vital issue back into the spotlight, then I am happy to be pranked on this occasion,” John wrote.
On the 11-minute call, John, 68, through a Russian translator, can be heard discussing a visit to Moscow with a man he believed was Putin.
“Tell him I am extremely honoured that he is calling me,” he said. “It is a great privilege to be able to speak to one of the most influential people in the whole world. It’s amazing.
“Tell him he has made my day... It’s a very wonderful moment in my life.”
Elton said one of his main concerns around gay rights is the issue of violence against LGBT people.
However, he added that he would prefer to have a face-to-face conversation with the president rather than over the phone.
“I would welcome [dialogue] because things get done better when you see somebody and you meet them,” said John.
“If both our offices can find a convenient date where we can convene and have a really wonderful discussion... that would be a miracle. It would be fantastic, and it would be a dream come true.”
The pranksters claimed it was easy to get in touch with John.
The musician publicly offered to talk with the Russian leader after meeting Ukraine’s president Petro Poroshenko at a conference to lobby him about LGBT rights.
The pranksters said it seemed John was “waiting for that call, so immediately believed in the reality” of the conversation.