The government was braced for a tight battle after junior justice minister Phillip Lee, a personal friend of May's, resigned on Tuesday morning in order to back the veto amendment.
"I absolutely trust what the Prime Minister says to us", he told BBC Radio 4's PM programme.
Some lawmakers tried to shout him down and accused the government of wanting too much power.
Parliament has been debating the EU Withdrawal Bill since September 2017, something which has taken up over 150 hours of its time. Several pro-EU Conservative lawmakers said they would join the opposition in voting against the government.
Britons voted 52 percent to 48 percent in favour of leaving the European Union in a June 2016 referendum.
But that vote required last-minute concessions to pro-European Tories, and they warned Wednesday they could yet seek to defeat the government if May fails to fulfil her promises.
A Brexit department spokesman said Tuesday, "We have not, and will not, agree to the House of Commons binding the government's hands in the negotiation".
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A statement by the Department for Exiting the European Union, led by Brexit Secretary David Davis, insisted that "we have not, and will not, agree to the House of Commons binding the Government's hands in the negotiations".
"The amendment passed in the Lords and accepted today by the Government states that there can be no physical infrastructure introduced between Northern Ireland and the Republic following exit day, and that nothing in the act can diminish full North-South cooperation".
The parts of his amendment which he expects to be taken forward by ministers provide a mechanism by which Parliament has to be consulted by the end of November in the event of no deal or if a proposed agreement is rejected, he said. Mrs May yesterday indicated the government would submit its own amendment, but not one which would necessarily meet the rebels' demands. The difference in this particular case is the enormity of the issue in the context of Brexit and in a climate of suspicion and hostility from many on the Conservative backbenches towards their leader.
On the second day of debate on the UK's flagship Brexit legislation, ministers conceded changes on refugee policy after Brexit. "Putting a decision off doesn't make it any easier".
It was a second win for May after she persuaded rebels in her Conservative party on Tuesday to reject a Lords amendment that would have allowed parliament to block the government from leaving the European Union with no deal.
The other is the maximum facilitation, or "max fac", scheme that would use technology and a "trusted trader" plan to reduce post-Brexit customs checks.
If May is defeated in the House of Commons it will be yet another blow to a prime minister whose authority has been challenged several times since last year's election.
"Theresa May doesn't need the support of the DUP anymore because she can always rely on Manchester's Jeff Smith to whip the Labour party in line with her".