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, reported the Independent.
She disclosed that she had held 12 meetings in Israel with officials, businessmen, Netanyahu and the country's security minister.
In her resignation, Patel apologised and said her actions "fell below the standards of transparency and openness that I have promoted and advocated".
May dubbed Patel's decision to resign as "right".
The Prime Minister, in her reply, said: "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."
In August, Patel flew to Israel with her family for a 13-day visit, which she later described as a "holiday", paid for by herself.
She held two further meetings after her "holiday" in September, according to the reports.
Patel is the second cabinet minister to leave the government in a week after Sir Michael Fallon quit as defence secretary. (ANI)