The embattled politician told Britons to “watch this space” hinting a return to politics would soon be on the cards, following an appearance on This Morning alongside Ms Marney.
Mr Bolton was kicked out as leader after a vote of no confidence from party members on Saturday.
His fall from grace centred around his affair with 25-year-old model Ms Marney, who was later found to have sent racist text messages about Prince Harry’s fiance Meghan Markle.
Writing on Twitter, the party said: “Henry Bolton has tendered his resignation from UKIP.
“We wish him well in whatever it is that he chooses to do next.”
The ex-Ukip leader later tweeted: “Watch this space”.
Ms Marney was suspended by the party and later revealed to have said Mrs Markle had a “tiny brain” and would “taint” the Royal Family.
Mr Bolton, 54, confirmed he and 25-year-old Jo Marney were back together after he left his wife, and the couple were interviewed live on ITV’s This Morning today.
Ms Marney admitted her comments about Prince Harry’s future wife were “disgusting”, adding the private comments were “meant to shock” and “never intended to be put in the public domain”.
The pair “absolutely” denied suggestions they were “private racists”.
During the interview Mr Bolton was read a statement from his wife, who accused him of “abandoning” her and their children and describing the aftermath of their break-up in December as “horrendous”.
She claimed: “Rather than trying to protect the privacy of people whom he hurt so badly, my still-husband has given countless interviews proclaiming his feelings for his lover whilst still being legally married and up until very recently saying at the same time to me that he wants our family to have a second chance.”
Fans slammed the pair as “vile” and an “utter disgrace”.
Viewers were angry at the couple trying to “justify” their behaviour, rather than apologise.
One wrote on Twitter: “An utter disgrace I would not give them air time.” Adding that they were “out of touch with society”.
Another said: “Not sure trying to justify her comments made that any better. Unbelievable.”
A third wrote: “Something very wrong with that pair.”
Ukip members backed a no confidence motion by 867 votes to 500 on Saturday.
The party’s national executive committee (NEC), which triggered the no confidence vote, chose MEP Gerard Batten as interim leader.