Mr Johnson quit Mrs May's Cabinet on Monday last week, declaring that the plans for the UK's post-Brexit relations with Europe which she set out at Chequers would leave Britain a "colony".
The government's Trade Bill passed its final hurdle in the Commons by 317 votes to 286.
Labour Brexiteers Frank Field, Kate Hoey, John Mann and Graham Stringer - along with independent Kelvin Hopkins - voted with the Government.
"Very significant defeat of govt tonight on European medicines regulation amendment".
Twelve Tory "remainer" MPs rebelled against the party whip and backed the amendment while four Labour Brexit-supporting MPs rebelled against their party whip and backed the government.
The Conservative rebels were the long-time pro-EU MP Ken Clarke, Heidi Allen, Guto Bebb, Richard Benyon, Jonathan Djanogly, Dominic Grieve, Stephen Hammond, Philip Lee, Nicky Morgan, Robert Neill, Mark Pawsey, Antoinette Sandbach, Anna Soubry and Sarah Wollaston.
Pro-EU lawmakers - from both May's Conservatives and the opposition Labour Party - want Britain to join a European customs union if there is no trade agreement with the bloc by January, two months before Britain is due to leave.
The Chequers agreement, named after the prime minister's countryside retreat, shifted the government's position in a soft Brexit direction.
The statement also won support from Nigel Farage, but the former Ukip leader made clear he did not believe the Brexit desired by Mr Johnson could ever be delivered by Mrs May.
Ms Soubry suggested that those MPs who favoured Brexit were uncaring fat cats sitting on huge pensions and condemning swathes of the country to poverty and unemployment.More news: Thunder trade Anthony to Hawks, waiver likely
The former London mayor was the face of the Brexit campaign in 2016.
"He has made an accusation in this house against individual members of this house and of the government.
This Government will never stand for that", she said.
A strong rebellion on the Conservative benches could lead to an embarrassing defeat for a Government now assailed on all sides over its plans for leaving the European Union.
"That was the vision that the Prime Minister rightly described previous year".
"Each day that ministers waste arguing amongst themselves increases the risk of the United Kingdom crashing out of Europe without an agreement".
Umunna said the four had helped May avoid a humiliating reverse over the customs union vote. It would remove our ability to have an independent trade policy at all, conceding Britain's role on the global stage as a force for free trade and endangering people's jobs and livelihoods. By implication, she suggested anyone who voted to leave the European Union was also uncaring, or else ignorant.
After the hubbub had abated, Mr Corbyn continued: "Isn't it the case that the Government is failing to negotiate Brexit, failing to meet the needs of the country because they are far too busy fighting each other?" We - that is MPs from every party - would be working against the Tories.
The Government said it would "revisit" the EMA amendment when it comes before the House of Lords.
"We would look to be an active participant and this would involve making an appropriate financial contribution".