But just an hour before the vote, due at around 1500 GMT, the government sought to compromise with senior pro-EU Conservative lawmaker Dominic Grieve, who had put forward his own amendment, which increased the risk of a government defeat.
A dispute quickly arose about the third clause of Grieve's amendment, with Brexiters, including some ministers, quickly saying all that had been agreed was talks - and no government could agree to be "directed" by MPs.
He added: "The reality is if we don't have a mechanism by which this House can properly shape the crisis that will be enfolding us at the end of February if we haven't got a deal, then we will do it in an ad hoc way which is likely to be infinitely more damaging to the well-being of the citizens of the United Kingdom".
"We had a personal assurance that we would find a way of addressing the concerns which are encapsulated in these amendments", Mr Grieve said as voting continued on Tuesday.
"We have not, and will not, agree to the House of Commons binding the government's hands in the negotiations". "I'm fairly confident we will be able to do that". The House of Lords has inserted 15 amendments to soften the terms of Britain's departure.
She said unless there was a "meaningful vote" Parliament would be left with "the grim choice between a poor deal and exit with no deal at all". "I can not support the government's decision to oppose this amendment because doing so breaches such fundamental principles of human rights and parliamentary sovereignty", he said.
Prior to the votes, the government suffered its first ministerial resignation over Brexit as Phillip Lee quit the Ministry of Justice so he could speak out freely.
"If, in the future, I am to look my children in the eye and honestly say that I did my best for them I can not, in all good conscience, support how our country's exit from the European Union looks set to be delivered".
Phillip Lee, who resigned this morning, gave an impassioned speech from the "naughty corner" on the backbenches - flanked by Remainers including Bob Neill, Nicky Morgan, receiving congratulations for his decision by Soubry and Sarah Wollaston.
Britons voted 52 percent to 48 percent in favor of exiting the European Union in a June 2016 referendum.
Ahead of the crucial votes, Brexit Secretary David Davis warned MPs that defeat would undermine the UK's negotiating stance in Brussels.
It sets up the prospect of frantic efforts by Mrs May to appease both Leave and Remain sides of her parties, as well as another potential crunch vote in the House of Commons next week.
The most contentious was the bid to give Parliament the power to tell the government what to do if the Brexit deal was voted down or no agreement was reached.
He said: "Facing the prospect of a humiliating defeat, Theresa May has been forced to enter negotiations with her backbenchers and offer a so-called concession".
Details of the government's commitment will have to be formalised next week in a new amendment to the bill.