The West Midlands MEP has vowed to back victorious Henry Bolton "to the hilt" after the former policeman and army intelligence officer won the leadership election with 30 per cent of the vote.
Based in Folkestone, the former soldier and police officer was considered to be a front-runner in the contest and had seen the odds on him winning fall dramatically in recent weeks.
And it saved Ukip, whose support evaporated in the June general election, from the total collapse that would have been triggered by a Waters victory.
The party has riven with tensions since then and some commentators said a party set up to oppose European Union membership had lost its reason to exist, particularly after the charismatic Farage stepped down. She came second, with Bolton gaining over 1,000 more votes than her.
Waters' defeat indicates the party is likely to keep its focus on Brexit instead of expanding it to include Islam.
Mr Bolton, who lives in Folkestone and stood as the party's candidate in last year's Kent police and crime commissioner election, was fourth favourite for the top job going into the conference in Torquay, but beat off the favourites - anti-Islam campaigner Anne Marie Waters and London Assembly member Peter Whittle - to win with 3,874 votes.
"Brexit is our core task", Bolton announced.
"If you look at the things I've done, you'll see a certain degree of endurance there, both physical, emotional and political", he said.
Bolton went further and claimed that Ukip would be in danger of becoming the "UK Nazi party" if it chose the wrong leader.
Henry Bolton has been named leader of UKIP. Bolton reportedly said he was "fine" with the new design.
"There is no greater calling than that and I would call on all of you, whether you voted for me or not, to rally around the party, to be united".
The party has been riven by splits and disagreements, one of which resulted in MEP Steven Woolfe being taken to hospital after a fight with another Ukip MEP. She resigned after just 18 days in the post, saying she could not work with the party hierarchy.