The support of the most Euroskeptical sector of the Conservative Party and of 19 rebel lawmakers from the Labor Party opposition gave Johnson a comfortable majority of 30 votes - 329 to 299 - in the House of Commons on Tuesday, Efe news reported.
Despite having given the green light to the terms of the pact, the members refused to deal in just three days with the law that would implement them - a dense text of 110 pages that the government published on Monday evening - as Johnson had been demanding.
Thar refusal frustrates the hopes of the prime minister to abandon the European Union on October 31, as he has promised to do on numerous occasions, at least in an agreed-upon manner.
Johnson said that he will continue with preparations for a possible abrupt break with the EU in nine days, although he emphasized that his intention now it to work to ensure that the divorce proceeds on the basis of the accord that has Parliament's approval.
His next steps will be determined once Brussels has commented on the delay that Johnson last Saturday saw himself forced to request.
The EU still has not responded to that request, in which Britain is once again proposing to delay Brexit, this time until January 31.
Although the uncertainty persists and the obstacles facing the accord are still numerous, Johnson has managed to overcome a hurdle that had stymied his Conservative predecessor, Theresa May, on three occasions.
"We should not overlook the significance of this moment," said Johnson, adding that just a few weeks ago, almost nobody thought that the House of Commons would approve the deal.
"One way or another we will leave the EU with this deal, to which this house has just given its agreement," he said
Labor Party leader Jeremy Corbyn, meanwhile, said he was in favor of agreeing with the Conservatives on a reasonable timetable to deal with the matter of transferring into British law the Brexit terms.
If the government decides to reactivate the ratification process, the text will still have to go through an amendment phase in the House of Commons.
In negotiating the country's exit from the EU customs area, the prime minister agreed to establish customs controls between Northern Ireland and the rest of the UK, known as the "Irish Sea border."
That stance motivated Northern Ireland's far-right Democratic Unionist Party, a parliamentary partner of the Conservatives, to announce its opposition to the Withdrawal Agreement and on Tuesday to vote against it.
( With inputs from IANS )