It ends days of speculation about the cabinet minister's position after she broke protocol to meet politicians, including Israeli Prime Minister Benjamin Netanyahu, without informing Downing Street.
Ms Patel arrived at Number 10 for an hour-long face-to-face meeting with the Prime Minister just after 6pm on Wednesday, having been ordered back to the country from Africa.
Earlier in the week, it had appeared she might avoid being pushed out after disclosing details of the meetings and apologising to Ms May. But it later emerged that she did not disclose all of the meetings that she had, angering Number 10.
In a letter to the Prime Minister, Ms Patel said: "I accept that in meeting with organisations and politicians during a private holiday in Israel my actions fell below the high standards that are expected of a secretary of state.
"While my actions were meant with the best of intentions, my actions also fell below the standards of transparency and openness that I have promoted and advocated.
"I offer a fulsome apology to you and to the Government for what has happened and offer my resignation."
In response the Prime Minister reminded Ms Patel that cooperation between Israel and the UK had to take place "formally, and through official channels".
She added: "Now that further details have come to light, it is right that you have decided to resign and adhere to the high standards of transparency and openness that you have advocated."
It first emerged last Friday that Ms Patel had travelled to Israel over the summer and conducted a number of meetings and visits with Israeli officials and politicians.
During the 13-day visit, which she described as a “holiday” paid for by herself, she was accompanied in meetings by Lord Polak, president of Conservative Friends of Israel, and discussed departmental business with key figures including the Israeli Prime Minister Benjamin Netanyahu.
It triggered accusations that she had ignored ministerial rules that she should tell the Foreign Office about business taking place overseas, and embarrassed Ms May who was kept in the dark about it for months.
When the trips emerged Ms Patel initially told a reporter that Boris Johnson’s Foreign Office had been informed, but later admitted in a statement that it was not.
Ms Patel also publically apologised and accepted that she had not acted in “accord with the usual procedures”, and was forced at a meeting with Ms May to set out all of the appointments she had in Israel, 12 in total.
Her public contrition appeared to have saved her political career, but over the next two days details of her trip and other meetings emerged that had not been shared with Ms May.
These included that she had discussed the idea of handing UK aid cash to the Israeli army to carry out humanitarian ops in the Golan Heights, that she had visited an Israeli field hospital there and that she had a further meeting with another Israeli minister, Gilad Erdan, in Westminster.
With opposition politicians calling for Ms Patel’s resignation and Ms May’ own actions being called into question, the new revelations and further embarrassment they caused sealed the minister’s fate.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies