Kokje will replace incumbent Raghava Reddy who is said to be close to VHP International President Togadia.
The voting to elect the new president was held for the first time in over five decades.
Reports say Kokje got 131 votes and defeated Reddy who could gather mere 60 votes. A total of 192 delegates of the VHP cast their votes in today's poll here.
The election was necessitated after the organisation members could not succeed in reaching a consensus on a new international president and also to induce transparency.
Togadia, who had a fallout with PM Narendra Modi, had hinted in an interview with ABP News that the elections are being carried out only to oust him. He also slammed the Modi government for not enacting a law to build the Ram temple at the disputed site in Uttar Pradesh's Ayodhya.
Rubbishing Togadia's allegations, VHP leader Surendra Jain said "the election was conducted to understand the viewpoint of the members and not intended to defeat someone. Everyone respects that and was held in a fair manner. There was no pressure on the organisation to hold election. You can defer an election under pressure but can't organise one."
Togadia quits VHP
In a press conference post election, Togadia congratulated Kokje for becoming the new president but said he has "left the organisation" after strengthening it in the past few decades.
He announced an indefinite fast from April 17 which is aimed at fighting for rights of Hindus, rehabilitation of Kashmiri Pandits and nations' farmers. He appealed his supporters to maintain calm.
It wasn't clear whether he might launch a new outfit.
Earlier this year, Togadia had gone missing for around 10 hours. He emerged from a private hospital and alleged PM Modi of conspiring with Gujarat Police to harass him. He also claimed there was a conspiracy to kill him by the Crime Branch and the Rajasthan Police.
Togadia had called Modi his "old friend" and urged him not to take steps that would lead to killing of democracy.
About Vishnu Sadashiv Kokje
Vishnu Sadashiv Kokje belonging from Madhya Pradesh was the Governor of Himachal Pradesh between 2003 to 2008. He reportedly held the post of acting Chief Justice of Rajasthan High Court for around 11 months in the year 2001. He also worked as senior judge in the Supreme Court in 2002.