Pavel Durov who ran VKontakte had previously announced he was leaving the company but said he had withdrawn his resignation.
The company denied it had been withdrawn.
Mr Durov had previously refused requests from the Russian government to censor posts on his site.
In a statement Mr Durov said that he only found out about the loss of his job from press reports: "Today I was fired as general director of VKontakte. It's interesting that the shareholders didn't have the bravery to do this directly, and that I learned about my firing from the press.
"Today VKontakte goes under the complete control of Igor Sechin and Alisher Usmanov. Probably, in the Russian context, something like this was inevitable, but I'm happy we lasted seven and a half years. We did a lot. And part of what's been done can't be turned back."
Clean conscience
Mr Sechin is the chief executive of state-owned oil company Rosneft and was President Putin's former deputy chief of staff.
Mr Usmanov, who is the richest man in Russia according to Forbes, made his money in iron ore and steel and until recently held a stake in Facebook. He has a large shareholding in VKontakte via his internet company Mail.ru.
Mr Durov announced his resignation publicly on 1 April but two days later said it was an April Fool's joke.
The Russian news agency Interfax reported that Vkontakte said they had acted on Mr Durov's resignation letter of 21 March as he had not withdrawn it officially within an allowed one-month grace period.
In an interview with news site TechCrunch Mr Durov said he was no longer in Russia and had no plans to return.
"Unfortunately, the country is now incompatible with internet business at the moment.
"I'm afraid there is no going back [to the company], not after I publicly refused to co-operate with the authorities. They can't stand me," he said.
The site has more than 100 million users and had been subject to several government requests for information.
Mr Durov had been asked by the Russian authorities to hand over the details of Ukrainians who had used the site to create groups related to anti-government protests. He was also asked to close down a group that supported Russian opposition leader Alexei Navalny.
He refused the request and said he sold his shares in the company so that he could continue "to make the right decisions".
"I have a clean conscience and ideals that I am willing to defend," he said in a post at the time.
Reports suggest that a replacement for Mr Durov will be elected at the next VKontakte board meeting.
Source: BBC News
