The amendment would have forced the Government to withdraw from any free trade agreement with any country which the High Court rules is committing genocide. Tory MPs wanted to use the changes, first put forward by the House of Lords, to ensure the Government did not sign a trade deal with China while Uighur Muslims are persecuted.
The Bill is a key part of Mr Johnson’s plans for Britain post-Brexit and sets out how the UK intends to trade on the world stage.
Senior Brexiteer Sir Iain Duncan-Smith led the Tory rebellion on the vote saying Uighur Muslims have been pushed into slave labour by Xi Jinping’s repressive Chinese regime.
Mr Johnson’s blushes were only just being saved with the proposed change to the Bill rejected by 319 votes to 308.
A total of 33 Tories backed the amendment and voted alongside Labour MPs.
Following the Government’s win, Sir Iain said he hoped the pressure from Tory rebels would force Ministers to rethink and urged the House of Lords to once again introduce the amendment.
He said on Twitter: “Today’s rebellion shows the Govt can’t ignore calls to bring genocide cases before UK courts.
“We’ll continue to work on this amendment, considering all points MPs made today.
“I hope the House of Lords will ensure an improved amendment returns to the House of Commons.
“The willful ignorance of alleged genocide and grave human rights abuses in China and elsewhere must stop, we will not sell out our values for trade deals with genocidal states.”
Senior Conservative backbencher Tobias Ellwood, chairman of the Commons Defence Committee, was another senior Conservative to back to so-called “genocide amendment”.
During a debate on the Bill, trade minister Greg Hands said the Government wants to hold “further discussions” with Conservative MPs on how to approach concerns over genocide when developing trade deals.
But he angered them by admitting he had not read a compromise amendment, which was tabled by Sir Iain and Conservative MP Nusrat Ghani and designed to avoid a rebellion by containing the thrust of proposals introduced by peers while easing Government concerns.
In the Commons last week, Foreign Secretary Dominic Raab dismissed the amendment as “well-meaning” but also “rather ineffective and counter-productive”.
Ahead of the vote Ms Ghani said the UK must not be “complicit” with genocide.
“Britain must be on the right side of history.
“This is our first chance outside the EU to show what our values really mean and what global Britain stands for,” she said.
“Why would we want to use our newfound freedom to trade with states that commit and profit from genocide? Britain is better than that.
“As we form trade deals with new partners, we must honour our sacrosanct responsibility never to let economic concerns trump ethical ones by dealing with genocidal states.”
The vote on the amendment came on the same day the Trump administration in the US accused China of committing “genocide and crimes against humanity” by repressing Uighur Muslims.
On his last day in the job, Secretary of State Mike Pompeo said “after careful examination of the available facts,” the US had reached the conclusion genocide had been committed since at least March 2017.
He said: “I believe this genocide is ongoing, and that we are witnessing the systematic attempt to destroy Uighurs by the Chinese party-state.”
China has dismissed reports of mistreatment of Uighur Muslims as “lies”.