Backed by former UKIP leader Nigel Farage to turn the party's fortunes around, Bolton was instead humbled by party members, when 63 percent of 1,378 ballots cast at an Extraordinary General Meeting were for his removal.
Mr Bolton said he still has "strong affections" for his former girlfriend who sent offensive messages about Meghan Markle, and compared the scrutiny of his private life to that faced by Diana, Princess of Wales.
Outgoing party chairman Paul Oakden told delegates to remain faithful to the party regardless of the decision.
HENRY BOLTON, the current leader of UKIP is to be ousted.
Bolton's position became increasingly precarious after it emerged he had left his wife for Ukip activist Jo Marney - a move which some in the party felt undermined his "family man" image.
Marney, 25, who was also a UKIP member, was suspended from the party at the time.
Speaking after the result, Mr Bolton said he had not finished in politics and was "batting around" various options for the future.
Mr Bolton had attempted to cling on to the leadership despite a no confidence vote by the ruling national executive committee (NEC) and a revolt by several senior figures in the party in protest at his relationship with model Jo Marney.
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"We matter now more than we ever have", he said.
"We still have to get a clean Brexit".
"The alternative is for the party to carry down the path of self-destruction into irrelevance".
Writing prior to the vote Cllr Chris Wells, the leader of TDC - the country's only UKIP council - said: "Whilst a leadership election is nobody's first choice, it is, at least, an election with rules and equality of franchise".
"It may be too late to save UKIP, but you never know".
Bolton was the party's sixth leader in 18 months when he was appointed past year.
The bookies' favourite is East of England MEP Tim Aker, followed by London Assembly member David Kurten and - despite having insisted he will not return again - Mr Farage.
Henry Bolton had only been in post since September 29.