In a devastating assault, Mr Johnson accused the PM of misleading voters about her intentions and putting the United Kingdom "in limbo" with the Chequers plan she forced through Cabinet.
On Tuesday, it was the turn of the softer, pro-European conservatives in her ranks who put her to the test, as she narrowly averted defeat in a parliamentary vote that signaled the potential for months of gridlock over the country's tortured efforts to extract itself from the bloc.
The prospect of continued drama in parliament and doubts over the future of May's "white paper" Brexit plan - which is only a starting point for talks with the European Union - is testing the patience of businesses that depend on cross-border trade.
The Commons was only half full for the statement but Johnson was surrounded by eurosceptic members of the ruling Conservative party, including David Davis, the former Brexit minister who also quit the cabinet last week over May's plan.
The legislation change would have committed the United Kingdom to joining a customs union had it not been able to strike a free trade deal with the EU by January 2019.
As noted by the BBC, some critics of Theresa May regard Johnson, a former London mayor, as a possible successor, should she be forced out over Brexit.
The prime minister's white paper, which is based on the Chequers agreement, envisages a deal with the European Union whereby Britain would keep regulatory alignment with the bloc on goods while having more flexibility on services, which represent 80 per cent of the British economy.
May's plan has drawn criticism from members of her party as well as pro-Brexit members.
Writing in the Daily Telegraph Mr Timothy said that if Britain leaves the European Union in "chaos" or does not leave the bloc at all, "a national humiliation greater than Suez awaits".More news: Microsoft unveils new Surface Go, its smallest and cheapest tablet yet
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Junior Defense Minister Guto Bebb, who'd supported May's initial plan, objected to the new plan and also resigned.
Mr Clarke said he had withdrawn a letter calling for a confidence vote in Mrs May because Brexit had taken the Tory party to "breaking point", stating: "We have looked into the abyss in the last few days".
However he denounced the plan agreed at Chequers and set out in the PM's white paper last week as a "Brexit in name only" which would leave the United Kingdom in a state of "vassalage".
"It is as though a fog of self-doubt has descended", Johnson said.
Ms Soubry said she did not believe Mrs May was in charge any more.
May said she would seek a "bold, ambitious and comprehensive" free trade agreement with the EU outside the customs union and single market.
He urged the government to "explicitly aim once again for the glorious vision of Lancaster House" instead of the "miserable permanent limbo of Chequers".
Even such a small change could be important - if 48 legislators submit letters seeking a confidence vote on May's stewardship of the party, it automatically triggers a leadership vote.