His resignation came hours before British Prime Minister Theresa May faces crunch votes in parliament and a potential showdown with pro-EU rebels in her ruling party over whether parliament can prevent a no-deal Brexit.
The U.K. government has agreed to give parliament more power over its Brexit negotiations in a last-ditch bid to avoid a damaging House of Commons defeat.
The European Union Withdrawal Bill, a complex piece of legislation meant to disentangle Britain from the bloc, has had a rocky ride through Parliament.
The new amendment, proposed by Conservative MP Dominic Grieve, will now be considered when the bill returns to the House of Lords, with government whips indicating to the rebels that they will accept the bulk of the amendment.
Her fellow Conservative backbencher Stephen Hammond said: "Parliament must be able to have its say in a "no deal" situation".
It is believed the deal will see parliament playing a bigger role in Brexit negotiations if there is no deal by November 30 this year.
As the Brexit debate reached its fraught climax, she was holed up in the same House of Commons office, behind the Speaker's chair, where she spent more than an hour last Thursday trying to convince David Davis not to resign.
A Lords amendment to the EU Withdrawal Bill would have given MPs the decisive say on what happens over Brexit if they don't agree with the final deal with the EU.
In a painful blow the the PM, Remain-supporting MP Philip Lee quit as justice minister this morning, saying he could not support "how our country's exit from the European Union looks set to be delivered".
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"But if the Lords amendments are allowed to stand, that negotiating position will be undermined".
Brexit protesters outside Parliament House.
May's government is divided between Brexit-backing ministers such as Foreign Secretary Boris Johnson who support a clean break with the European Union, and those such as Treasury chief Philip Hammond who want to keep closely aligned to the bloc, Britain's biggest trading partner.
Despite many Conservative MPs who backed Remain in the referendum, just two rebelled against the government on a meaningful vote.
Britain's highest-selling tabloid, The Sun, which is owned by Rupert Murdoch, addressed lawmakers directly on its front page, saying they faced a choice between "Great Britain or Great Betrayal". The Daily Express thundered: "Ignore the will of the people at your peril".
It is the legislation aimed at ensuring the United Kingdom has a smooth transition out of the EU.
"That was the decision of the British people. and whatever we do, we're not going to reverse that", he told the BBC.
He confirmed that ministers will seek to overturn 14 amendments which he said would undermine the goal of the Bill and fail to respect the result of the 2016 referendum.