But Bercow defended himself against a torrent of criticism, telling the Commons he needed ‘no lessons or lectures’ on how to do his job.
He said he had made an honest judgement and would carry on doing his duty ‘no matter how much abuse I get.’
The vote, tabled by Tory Dominic Grieve and approved by Bercow, resulted in the second defeat in two days for the government, this time by 11 votes.
It means ministers must now come up with a ‘plan B’ within three days, rather than three weeks as previously agreed, if Mrs May’s Brexit deal is rejected by MPs next week.
Leader of the Commons Andrea Leadsom said afterwards that Bercow’s actions were ‘extremely concerning.’
She was one of a number of MPs who challenged his ruling and sought clarification as a series of points of order were raised after Prime Minister’s Questions.
Leadsom later appeared on ITV’s Peston show and said Bercow had set a ‘damaging precedent’ that could affect future legislation in the Commons.
“The Speaker, instead of being the guardian of the rules, decided to unilaterally change the rules… It doesn’t just damage me, it damages all of Parliament.”
Tory Jacob Rees-Mogg said he disagreed with the Speaker’s decision but that Bercow was ‘a House of Commons champion’ and the amendment was ‘irrelevant.’
Former minister Crispin Blunt questioned whether Bercow was still a ‘neutral referee of our affairs’ as the Speaker is supposed to be.
Bercow rejected calls to publish his clerks’ advice on the vote and said if Parliament was always bound by precedent ‘nothing would change and things do change.’
He said he was ‘championing the rights of the House of Commons’ and MPs could vote against the amendment if they wanted to.
Bercow, MP for Buckingham since 2007, has been speaker for almost a decade and has frequently been at the centre of controversy during that time.