Around 30 Conservative MPs were thought to be preparing to vote for the amendment on Tuesday which would have required a Commons vote before the provisions in the Bill relating to Northern Ireland could come into force.
Ministers were said to be hoping they could defuse the revolt by agreeing to provide an “extra level of parliamentary scrutiny”.
Earlier European Commission president Ursula von der Leyen, warned the UK could not unilaterally set aside the Withdrawal Agreement which settled the terms of its “divorce”.
In her annual State of the Union address to the European Parliament, Mrs von der Leyen said both sides had agreed it was the only way to guarantee the Northern Ireland peace process.
Mr Johnson has insisted the Bill is intended to provide a legal “safety net” to protect the peace process and ensure the EU could not impose tariffs on goods moving to Northern Ireland from the rest of the UK.
Addressing the Parliament in Brussels, Mrs von der Leyen said: “This Withdrawal Agreement took three years to negotiate and we worked relentlessly on it line-by-line, word-by-word, and together we succeeded.
“The European Union and the UK jointly agreed that it was the best and only way for ensuring peace on the island of Ireland and we will never backtrack on that.
“This agreement has been ratified by this house and the House of Commons. It cannot be unilaterally changed, disregarded or disapplied.
“This is a matter of law and trust and good faith.”