John Bercow can sometimes seem to be auditioning to play Shakespeare’s Malvolio. The House of Commons Speaker has at times a comic degree of self-esteem that is the equal of the arrogant steward in Twelfth Night. Like Malvolio, Bercow can also drive colleagues to distraction, as he did today. Today, though, Bercow took a brave stand to empower Britain’s parliament against Britain’s government on Brexit. And that qualifies him to be considered the most radical holder of his office in generations. Like Malvolio, a version of greatness has been thrust upon him.

The vast majority of people are understandably not well versed in Commons procedure. So it may seem strange to claim that a decision to allow an amendment to be moved on a Commons timetable motion – and with no debate – is in any way immense. Nevertheless, Bercow’s decision to allow the all-party effort, led by the Conservative former attorney general Dominic Grieve, to tie the government’s hands – it must come back with a plan B within three days if the Brexit deal is defeated next week – deserves such accolades.

Theresa May is increasingly having her Brexit options shaped for her by a cross-party alliance of MPs

The 11-vote victory for Grieve’s amendment may be pivotal in the Brexit endgame. Coming on top of Tuesday’s seven-vote government defeat on the Yvette Cooper no-deal motion, it is confirmation that Theresa May does not have a majority for her Brexit deal. The path lies open – though the intervening ground remains treacherous – towards either a softer “Norway plus” relationship, or a second referendum that may lead to Britain remaining in the EU after all.

None of this would have happened, or even be a possibility, under a more deferential Speaker than Bercow. And it only happened because he has consciously put himself in the front line, over the most important issue of our time, in a long battle to strengthen the power of parliament against ministers. The Speaker may have come to this partly for reasons of his own vanity, or because he dislikes the House leader Andrea Leadsom, or because, with his time as Speaker likely to come to an end this year, he is willing to go out with all guns blazing. But there are far bigger issues at stake in his action too.

Play Video 1:32 'That sticker is not mine': John Bercow forthright about wife's anti-Brexit sticker – video

Bercow took his stand because Brexit has presented modern parliamentary politics with a choice that, in the end, it could not avoid. On the one hand, the Commons could do what modern British parliaments have normally done and, after much huffing and puffing, allow the government to get what it wants. On the other, it could do what parliaments too rarely do, but which many non-partisans have longed for it to do and, working cross-party, drag down the power of ministers and all the patronage and power at their disposal.

The confrontation between MPs and ministers that consumed Westminster today was not ultimately caused by Bercow’s ego. It was caused by the convergence of the immensity of Brexit – which threatens to reshape the economy, politics and international standing of Britain in massive ways – and the reality that May leads a deeply divided party and government in a hung parliament where there is no majority for anything without formal or informal cross-party alliances. In such circumstances, the old rules were always likely to buckle and bend; and they did so.

Facebook Twitter Pinterest Theresa May during prime minister’s questions on 9 January. Photograph: Mark Duffy/AP

Parliamentary sovereignty has always been significantly qualified, ever since the Glorious Revolution of 1688-89 laid its modern foundations. Parliament is not in practice a collective Athenian-style assembly that does whatever it chooses, though its powers are sweeping. Parliament is a legislature that is controlled and structured to benefit the executive – even a weak one such as May’s. Parliament’s sovereignty is managed by ministers on behalf of the crown, today as in 1689. It was against this that Bercow took his stand.

Over the years there have been repeated complaints – particularly, of course, from the opposition – that parliament’s sovereignty is being systematically gelded by ministers. Under governments of every kind, Labour as well as Conservative, ministers have tightened their grip over backbenchers through systems of appointments, control of the agenda, delegated powers, and timetabling. The growth of the career politician, often at the expense of MPs with wider experience, has made the job of control easier.

There has always been some pushback – in the growth of more independent select committees, for example. But it has taken Brexit added to a hung parliament to lift the counter-movement to this new level, in the run-up to the Brexit showdown on 15 January. The implication of Bercow’s decision to call Grieve’s amendment – against the advice, it seems, of his clerks – is that governments will now find it more difficult to control the parliamentary timetable.

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There is no suggestion that Bercow’s ruling guarantees a better Brexit outcome. Still less that it will open the floodgates to parliament setting its own agenda more generally, or to the Speaker writing the Queen’s speech – backbench power has more purchase in a hung parliament than one with a landslide majority, and Brexit is a uniquely important and divisive issue. But the breach in ministerial control has been made all the same. And we have gone, in less than two years, from May’s attempt to implement Brexit without any parliamentary involvement, to a position in which the prime minister is increasingly having her Brexit options shaped for her by a cross-party alliance of MPs.

These MPs are, moreover, an exceptionally able and talented bunch. They eclipse many on their own frontbenches. You could almost say that the real leaders of the Tory party are now Nicky Morgan and Nick Boles, while the effective leaders of Labour this week were Yvette Cooper and Stephen Kinnock.

It would not, of course, be quite true. The parties and their leaders remain the key players. Nevertheless, a new and more rational form of parliamentary politics is evolving around the old parties. The faith-based politics of left and right is struggling to respond.

This is not to claim that faith is unimportant or that pragmatism will triumph. But pragmatism is having a good run, against the odds and in the most important of circumstances. It will surely leave a deep mark, not just on the Brexit outcome next week but also on the politics of the near future more generally. Amid so much failure elsewhere in our political system, this seems worth cherishing and cheering.

• Martin Kettle is a Guardian columnist