Johnson, though, said it was essential to counter "absurd" threats from Brussels including that London put up trade barriers between Britain and Northern Ireland and impose a food blockade - steps he said threatened the UK's unity.
"The EU still have not taken this revolver off the table", he told parliament before the vote.
A number of Conservative former ministers made clear that they would not support any measure which breached global law, including Andrew Mitchell, Sir Oliver Heald and another former attorney general Jeremy Wright.
The Internal Market Bill, created to govern trade within the UK's four nations, gives United Kingdom ministers powers to modify or "disapply" rules relating to the movement of goods that will come into force from 1 January, when the United Kingdom leaves the EU's single market, if a successor trade agreement is not reached. It's about exit declarations - Northern Ireland to GB - and the definition of state aid relating to Northern Ireland.
"Breaking worldwide law is a step that should never be taken lightly", wrote Tory MP and former chancellor Sajid Javid in a statement, adding that he could not support "pre-emptively reneging" on the withdrawal agreement and that he would not be supporting the bill on its second reading on Tuesday.
Sir Roger said: "I took a view that you fight this tooth and nail at every step. There is much to play for yet", he told BBC2's Newsnight.
"What this Bill is not doing is not walking away from negotiation with the European Union. Those negotiations go on", Mr Gove told the Commons.
He said it erodes trust and makes complex negotiations even more hard. Should the Lords oppose the bill, they could delay it by one year.
He claimed the Northern Ireland Secretary had "answered the wrong question" when speaking to MPs (see video below), and "as a outcome the whole matter has been taken out of context".
Labour's Ed Miliband, deputising for party leader Keir Starmer who was forced to self-isolate at home, accused Johnson of "legislative hooliganism" for threatening to break a treaty that he had negotiated and successfully won an election campaigning on.
"Either he wasn't straight with the country about the deal in the first place or he didn't understand it".
A wrecking amendment was defeated shortly beforehand, though more will follow as he faces a growing rebellion in his party.
"Because a competent government would never have entered into a binding agreement with provisions it could not live with".
The government welcomed the Commons vote to give the UK Internal Market Bill a second reading, saying that it was now critical that the legislation completed its passage through Parliament by the end of the year.
"When it comes to preserving the integrity of the United Kingdom and clearly delivering for the people of Northern Ireland when it comes to the Good Friday Agreement, we've said from day one. that we would always stand by our word and not compromise when it comes to unfettered access in goods and services but also standing by the Good Friday Agreement", she said on BBC Breakfast.
"I will therefore regretfully be unable to support the bill at its second reading and urge the government to amend it in the coming days".