While a parliamentary technicality, it led to a vote in which another tranche of Tories rebelled, 17 this time, and which means that rather than having 21 days to come up with a Plan B if her deal is rejected next Tuesday - as is widely expected - the Prime Minister will have just three.
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By forcing through a controversial amendment on Wednesday he has spurned the will of the government, possibly altered the course of Brexit by placing more power in the hands of those who wish the U.K.to remain in Europe, and made Prime Minister Theresa May's position more precarious.
The assurances are expected to be delivered in an exchange of letters on the eve of next Tuesday's vote - but the European Union has not so far found a form of words which would provide the game changing boost needed by May to win the vote.
The outcome of the crucial vote, which was pulled before Christmas when it became clear the Prime Minister would be defeated, could determine the fate of her Government.
On Wednesday, MPs approved a motion that will force her to return to Parliament with a "Plan B" within three sitting days of Parliament, or Monday.
"It is shameful that Corbyn continues to sit on the fence on the biggest issue this country has faced since the Second World War", Mr Tom Brake, spokesman on Brexit for the Liberal Democrats, said in a statement.
Mr Bercow admitted there was no precedent for his decision, but told MPs that centuries of convention did not "completely bind" him.
Opposition lawmaker Yvette Cooper said it showed the strength of concern about the dangers a no-deal Brexit could pose to manufacturers, jobs, food prices, policing and security.
The government said it was an "inconvenience" but would not stop preparations for leaving the EU.
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The government also lost on Tuesday night when another amendment curbing its financial powers in the event of "no-deal Brexit" without authorisation from parliament.
Late on Tuesday, legislators backed an amendment to the Finance Bill that puts roadblocks in the way of government spending on no-deal Brexit measures.
No 10 is now considering accepting an amendment tabled by Leave-supporting Labour backbencher John Mann that would provide for additional safeguards on workers rights and environmental protections.
Many Brexiter MPs were furious with Bercow, believing it was effectively unconstitutional to allow a business motion - which sets out what MPs are about to debate and vote on - to be amended.
May has repeatedly ruled out delaying Brexit, though she has also warned British lawmakers that if they reject her deal then Brexit could be derailed or the United Kingdom could leave without a deal.
It is not an absolute block to leaving the European Union without a deal because it does not negate the legislation already in place stating that Britain will leave the European Union on March 29.
Parliament is due to vote on the divorce deal next week.
Britain's de-facto deputy prime minister, David Lidington, said politicians must abandon "fantasies about magical alternative deals that are somehow going to sort of spring out of a cupboard in Brussels".
In the Commons, Tory anger was directed towards Mr Bercow who many MPs have long suspected is unduly sympathetic to the Remain cause.
The leader of the opposition Labour party, Jeremy Corbyn said: "This vote is an important step to prevent a no-deal Brexit".