Theresa May ordered Ms Patel to return from an official trip to Africa following the revelation of her undisclosed meetings with Israeli politicians.
She reportedly only made it as far as Nairobi, Kenya, before being told to return to the UK where she arrived on Wednesday afternoon for a meeting with the Prime Minister.
In her resignation letter, Ms Patel said it had been a “tremendous privilege” to serve in Mrs May’s Cabinet.
“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,” she said, adding that she acted with the “best of intentions”.
Ms Patel said she offers a “fulsome apology to you and the Government for what has happened and offer my resignation.”
She went on to say that she would continue to support the Prime Minister and the Government and “stand up for the Conservative values of freedom, opportunity and aspiration.”
In response to her letter of resignation, Mrs May told Ms Patel “it is right that you have decided to resign and adhere to the high standards of transparency and openness that you have advocated”.
“As you know, the UK and Israel are close allies, and it is right that we should work closely together. But that must be done formally, and through official channels,” she said.
Ms Patel had been under scrutiny after failing to inform either the Foreign Office or Downing Street about 12 meetings she held with top officials during a 13-day “family holiday” to Israel in August.
In fresh revelations, it is understood Ms Patel met Israel’s public security minister Gilad Erdan in Parliament on 7 September and foreign ministry official Yuval Rotem in New York on 18 September.
Mrs May was reportedly told about the New York meeting on Monday but only learned about the meeting with Mr Erdan on Tuesday.
Downing Street sources denied reports Ms Patel was told not to reveal her meeting with Mr Rotem in a list she published earlier this week.
Posting on Twitter at the time of the 7 September meeting in Parliament, Mr Erdan revealed he and Ms Patel discussed how “to advance UK-Israel development cooperation”.
When conducting official work overseas, ministers are supposed to tell the Foreign Office.
Ms Patel’s meetings included talks with Israeli Prime Minister Benjamin Netanyahu, a meeting Mrs May had no knowledge of for more than two months.
The Witham MP missed a parliamentary grilling over the exposure of those meetings on Tuesday, when she caught a flight to Uganda for a Government visit.
It was left to her junior minister Alistair Burt to explain how, on returning from her Israel trip, Ms Patel had proposed giving departmental cash to the Israeli army for aid programmes in the Golan Heights, which was ruled “not appropriate”.
All Ms Patel’s meetings in Israel were arranged by Tory peer Lord Polak, the honorary president of Conservative Friends of Israel, who also sat in on most of the meetings.
Lord Polak is chairman of consultancy TWC Associates, whose clients include an Israeli defence company and technology firms.
Ms Patel, who had been touted as a future Tory leader, was ordered to Downing Street on Monday when the Prime Minister reminded her of ministerial rules – before information about further meetings emerged.
Ms Patel’s resignation marks the second departure from Mrs May’s Cabinet within the space of a week, after Sir Michael Fallon stood down amid allegations of inappropriate behaviour towards female journalists.
Foreign Secretary Boris Johnson is also under pressure after his comments about a British national imprisoned in Iran led to fears her sentence could be doubled.
Meanwhile, Mrs May’s deputy Damian Green is being investigated over allegations of improper conduct towards a female columnist, with officials also looking into claims “extreme pornography” was found on his parliamentary computers.
He denies the claims.