While no debate was allowed on the amendment, which had been put forward by former Tory Attorney General Dominic Grieve, MPs spent more than an hour raising points of order in the Commons to challenge the Speaker on his decision.
Crucially, it will allow MPs to table amendments to whatever motion May brings back, allowing the will of the Commons to be tested on Brexit "plan Bs" such as a second referendum or a Norway model much sooner.
The move essentially means that control over Brexit has begun to shift from the Prime Minister to MPs.
Numerous Labour MPs also came to his defence, with Labour MP Chuka Umunna tweeting: "In the Commons chamber now watching the spectacle of a bunch of Tory MPs, who argued for Brexit to reassert Parliamentary sovereignty, now objecting to the Speaker selecting a motion to be voted on that would empower the House of Commons".
The package, tabled by former minister Sir Hugo Swire, also places a legally-binding commitment on the Government to end the backstop arrangement within 12 months, and to seek assurances from the European Union that it will seek to do the same.
"The prime minister will be updating parliament tomorrow and she will be talking about the clarifications, the reassurances that parliament is seeking that the backstop will not be permanent".More news: Former LSU lineman has leg amputated after getting shot by dog
May's spokesperson said the government's advice was that Parliament could not change its so-called business motion which set out the procedure for the Brexit vote, but played down the impact of the vote for its overall plans.
The development came after 17 Tory rebels helped pass Mr Grieve's amendment by 308 votes to 297.
But EU leaders have refused to budge, insisting that the withdrawal agreement can not be renegotiated.
Effectively this constrains the government's ability to act to keep its taxation system working smoothly if it pursues a no-deal Brexit against the wishes of a majority in parliament.
But Mr Corbyn hailed the development as an "important step" to prevent a no-deal Brexit.
May told lawmakers that parliament had a choice: back her or risk Britain leaving the bloc without a deal - a scenario many businesses say would splinter supply chains and hamper investment in the world's fifth largest economy. And there is no clear majority in Parliament for any single alternate course.More news: Lady Gaga wins second Golden Globe award in her career
Labour said it would try to trigger an election by calling for a no-confidence vote in the government if May's deal is defeated next week.
"We're all focused in the government on winning parliamentary support in the vote that's coming up next week", he told reporters as he arrived at the meeting in Brussels.
A top European parliamentarian urged British lawmakers to show "responsibility" over the divorce deal.
News agency dpa reported that Weber said everyone must realize that a no-deal withdrawal would "lead to very hard, perhaps even chaotic situations".
Environment Secretary Michael Gove told Cabinet that those considering rejecting Mrs May's agreement in the hope of securing a better deal were like swingers in their mid-50s waiting for film star Scarlett Johansson to turn up on a date. This echoed his widely misinterpreted comment earlier this week, when accusing the Prime Minister of engaging in "Project Fear" - a reference to the futility and expense of no-deal prep, not the argument hard Brexiteers make that no-deal is nothing to be feared.More news: Nokia 8.1 Is Coming To Malaysia This Month for RM 1699