The Lords voted 349-221 in favour of an amendment to change the wording of the bill so that instead of ministers being able to use the Henry VIII powers where they consider it "appropriate", they would have to prove it was " necessary".
Mr Davis was speaking ahead of a meeting on Wednesday afternoon of a Cabinet sub-committee dubbed Mrs May's "Brexit war cabinet", which will bring together senior ministers to drive negotiations forward in the vital coming months.
The motion being debated on Thursday calls on the Government to include as an objective in negotiations with the EU "the establishment of an effective customs union between the two territories".
He said: "Amber Rudd appears to have let slip that discussions around the Cabinet table about negotiating a customs union with the EU have not in fact concluded".
Some MPs believe a show of support for a customs union would also open the door for parliament to back Britain staying in the EU's single market, another thing May has ruled out.
She could lose her job after a vote of no confidence.
It would also help avoid new checks on goods crossing the border between Northern Ireland and EU-member Ireland, which some fear could upset the fragile peace on the island.
The EU Withdrawal Bill sets the legal framework for Britain's exit from the bloc on March 29 next year, but faces an arduous battle in being approved by both Houses of Parliament, whose members predominantly oppose Brexit.
Last week the UK's Brexit negotiator, David Davis, cautioned that without a real idea of how the future trading relationship with the European Union would go, British parliament could reject any proposed Brexit deal.
Within an hour, amid a growing Twitterstorm in Westminster, Rudd used Twitter to clarify her comments.
He said to exclude a number of important European Union rights from domestic law would lead to a lack of certainty and continuity, providing a "recipe for confusion" after Brexit.
Media captionWhat is the EU customs union?
May is before anything a unionist, her aides say, and will not want to be the prime minister that splits the United Kingdom, with one suggesting she had looked at some form of customs deal along the lines of a union.
She said Labour was "more interested in frustrating the process and playing politics than they are in delivering a successful Brexit".