But within minutes of the narrow victory, May was rocked by a fresh resignation, this time of her defence minister Guto Bebb, who voted with Labour to oppose the Government.
May is now facing a possible rebellion from Brexit supporters in her Conservative Party who want her to ditch her plan when lawmakers vote on amendments to legislation on the government's post-Brexit customs regime on Monday.
The government, which does not have a Commons majority, has been under pressure from MPs on both sides of the Brexit debate. It could be debated by MPs when the bill returns from the Lords, they added.
With an ever-diminishing majority the United Kingdom government has resorted to drastic measures, proposing that parliament closes five days earlier than usual.
The Daily Telegraph reported more than 100 MPs had joined the group, more than double the 48 needed to submit letters of no confidence in the Prime Minister to force a leadership contest.
But the government was saved from humiliating defeat by three Labour MPs, Frank Field, Kate Hoey and Graham Stringer, voting with the Government and another dozen or so Labour MPs missing the vote for whatever reason.
Theresa May claimed the Chequers agreement had not been changed, but the climbdown has prompted a furious row across Conservative benches.
May's dismissal of the idea was prompted by a Conservative, Justine Greening, who wrote in the Times of London that the "only solution is to take the final Brexit decision out of the hands of deadlocked politicians" with a second vote, which would give citizens three options: sticking with May's vision of a "Soft Brexit", remain in the European Union after all, or leave the bloc with no deal.
Former Education Secretary Justine Greening called on Monday for a second referendum on Brexit.
Chief Conservative Whip Julian Smith has been "aggressively" pressuring Remainer rebels to back down amid escalating party tensions over a customs union bill.
Theresa May explaining her Chequers deal.
Defending his record in office he added "don't tell me that the United Kingdom is losing diplomatic influence" citing the worldwide response to the Novichok poisoning which saw 28 countries expel 153 "Russian spooks".
"The PM has set out on a number of occasions our position in relation to the customs union, which is that we will be leaving the customs union and she believes that that's what the British people voted for and it is important that we are free to strike independent trade deals around the world".
It gives the government the power to build new trade relationships around the world after the United Kingdom leaves the EU, and MPs who support staying in the EU's customs union are seeking to change its wording.
"I wanted the prime minister's Chequers agreement to be a workable compromise", she wrote in The Times.
Her office has said there will be no second referendum under any conditions.
Negotiations in the meantime are ongoing in Brussels this week.
"Cabinet is behind it, businesses have come out to support it and now we need to get on with negotiating with the European Union".