Waters, whose potential election had threatened to destroy Ukip, with many MEPs and members warning they would quit were she to win, finished second with 2,755 votes.
Speaking after his shock victory Bolton, who once stood for the Liberal Democrats, told the audience at the party’s annual conference in Torquay: “While Brexit is our core task, that greater goals, which is ongoing beyond the time that we leave the EU, that is our core purpose.”
Bolton, 54, was supported in the contest by former leader Nigel Farage. Mr Farage said: “I am delighted @_HenryBolton has won the UKIP leadership election. He is a man of real substance.”
David Kuerten finished in third place with 2,201 votes with John Rhys Evans coming fourth on 2,021.
Whittle – a former candidate for London Mayor and the deputy leader of the party – finished a surprise fifth with 1,413.