West Midlands MEP Jill Seymour and Yorkshire and North Lincolnshire MEP Jane Collins announced their resignations on Monday.
It is understood that a third Ukip MEP, Margot Parker, has also quit the party.
Ms Collins said Ukip's attitude to women was "disgusting" and said she wanted to spend the rest of her time as an MEP fighting to secure a "real Brexit", saying Mr Farage's new party is the "best way of achieving that".
She said: "To have people like Carl Benjamin on the list for the party is something I find disgusting, and to hear Gerard Batten on national TV yesterday defending this man's use of rape as 'satire' made me sick to my stomach.
"I know women who have been raped and the mental and physical destruction it wreaks on these victims and their loved ones is the opposite of satire: it is a tragedy.
"I have spent much of my time as an MEP and as a Ukip candidate standing up for the rights of women, including the victims of industrial scale CSE in Rotherham and other areas.
"It is simply impossible for me to stay in the party now and I will serve out the rest of my mandate as an MEP for the Brexit Party."
Ms Seymour said that under current leader Mr Batten, Ukip had moved to "the extreme right of politics".
"I am not walking away from the party's original core principles, but the present party's direction means it has walked away from me, and its original membership," she said.
"I shall now be sitting as an officially designated Brexit Party MEP for the remainder of my mandate in the European Parliament."
Ms Seymour, who resigned last year as the party's transport spokesman, added: "No one person should ever be bigger than a political party, but sadly I believe that Mr Batten will be instrumental in its demise."
Ukip said in a statement: "Both Jill Seymour and Margot Parker wished and expected to be placed at the top of their lists in their respective regions as of last Friday. Both gave £1,000 each in UKIP campaign donations this month.
"The Leader and the NEC panel reluctantly came to the conclusion that they had not honoured their commitments to the Party as described in the MEP Charter of 2013 and as such they were not reselected.
"UKIP is disappointed that they have chosen to side with its opponents, but their motivations are clear.
"UKIP is entering the Euro elections with the three loyal MEPs who have honoured their commitments, alongside a fresh slate of candidates. We expect to win big."
It follows the announcement last week that the sister of leading Tory Brexiteer Jacob Rees-Mogg, Annunziata, had left the Conservative Party to stand as a Brexit Party candidate in next month's elections to the European Parliament.