The Prime Minister, who is is facing a battle to survive after the number of rebels demanding he go reached 148, said the UK Government could now “move on” following a “convincing” and “decisive” result.
But Sir Roger Gale, who voted to remove the Prime Minister, said he would be very surprised if Mr Johnson was still in post by the autumn.
Despite winning the vote, Mr Johnson is now a Prime Minister diminished and lacking authority, with two crucial by-elections to come that could yet ultimately seal his fate.
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It came on a day that saw four of six Scottish Tory MPs publicly call for the Prime Minister to go, despite support from the Scottish Secretary Alister Jack.
Mr Johnson survived with a majority of just 63 after 211 MPs voted to support him, against 148.
Speaking just minutes after the vote outcome was announced, the Prime Minister said he was “certainly not interested in snap elections”.
Earlier, a defiant Mr Johnson had told MPs he would make more tax cuts if they kept him, but failed to offer specifics.
The Prime Minister also warned Tory splits risked the “utter disaster” of Sir Keir Starmer’s Labour entering Downing Street, propped up by the SNP.
He said: “The only way we will let that happen is if we were so foolish as to descend into some pointless fratricidal debate about the future of our party.
“I humbly submit to you that this is not the moment for a leisurely and entirely unforced domestic political drama and months and months of vacillation from the UK.
"Everyone understands the fiscal impact of Covid, the cost of clearing the backlogs, but the way out now is to drive supply side reform on Conservative principles and to cut taxes.”
While Conservative Party rules mean he is safe from a confidence vote for another year, 41 per cent of his own MPs having no confidence could yet spell the end of Mr Johnson’s premiership.
The Prime Minister had issued a late plea to Tory MPs to support him, warning “pointless” internal warfare could see them turfed out of office.
He took five questions during the meeting, two of which were “hostile”, a senior party source said.
The vote came amid rising fury over the Covid breaches linked to the Partygate scandal – something Mr Johnson had previously “humbly” apologised for.
Despite this, when asked about attending leaving parties that broke lockdown laws, the Prime Minister insisted he’d “do it again”.
The scandal prompted the Scottish Conservatives leader Douglas to say he “cannot in good faith” support the Prime Minister following the breach of Covid rules.
Confirmation of Mr Ross’s vote came after several U-turns, with his last position having been Mr Johnson should stay in place until after the war in Ukraine was over.
Confirming his position just hours before the vote, Mr Ross said: “I have heard loud and clear the anger at the breaking of Covid rules that we all did our best to follow, and even more so at the statements to Parliament from the Prime Minister on this topic.
“Having listened closely to people in Moray who re-elected me to represent them, and from many people across Scotland, now that this confidence vote is upon us, I cannot in good faith support Boris Johnson. My vote tonight will support the motion of no confidence.”
There was a further Scottish blow to the Prime Minister, with John Lamont resigning as PPS to the foreign secretary and voting against Mr Johnson.
He said: “Whilst I recognise that changes have been made in Downing Street, the unfortunate reality is that the Government has become overwhelmed by these events, to the detriment of my constituents and people across the United Kingdom.
"The amazing work that this government is doing in Scotland and across the UK is increasingly being overshadowed.”
Former Scotland secretary David Mundell also voted against Mr Johnson, as did fellow Scottish Tory MP Andrew Bowie.
Former foreign secretary Jeremy Hunt, who stood against Mr Johnson for the leadership in 2019, warned the Tories would lose the next general election if the Prime Minister was allowed to remain in post.
He said: “Having been trusted with power, Conservative MPs know in our hearts we are not giving the British people the leadership they deserve.
“Today’s decision is change or lose. I will be voting for change.”
The anger was not isolated to known rebels either, with former minister and loyalist Jesse Norman withdrawing support in a scathing letter describing the Prime Minister’s response to the Sue Gray report as “grotesque”.
He told the Prime Minister in his letter: “Recent events have served to clarify the position this country is in under your leadership, beyond any doubt, and I am afraid I can see no circumstances in which I could serve in a Government led by you.
“For you to prolong this charade by remaining in office not only insults the electorate and the tens of thousands of people who support, volunteer, represent and campaign for our party, it makes a decisive change of government at the next election much more likely.
"That is potentially catastrophic for this country.”
Tory former chief whip Mark Harper said if the PM stayed in post, he would be asking MPs to “defend the indefensible”.
SNP Westminster leader Ian Blackford MP claimed Tory MPs had “bottled it” when it came to the no-confidence vote.
"The UK is now stuck in limbo with a lame duck Prime Minister who has lost the confidence of the public – and more than 40 per cent of his own MPs – and is left limping around on borrowed time while the Tory party descends into bitter division,” he said.
"As for Douglas Ross, his position is completely untenable. If he had any principles or dignity, he should quit as Scottish Tory leader.”
A succession of Cabinet ministers appeared on TV to voice support for the Prime Minister before the vote, while Government colleagues and backbenchers also went on social media in a co-ordinated operation to bolster Mr Johnson’s position.
Brexit opportunities minister Jacob Rees-Mogg said victory by a single vote would secure Mr Johnson’s job.
He told Sky News: “One is enough. It’s no good saying that the rules of the party say something and then behind it unofficially there is some other rule that nobody knows and is invented for the purpose.”
Foreign secretary Liz Truss said: “The Prime Minister has my 100 per cent backing in today’s vote and I strongly encourage colleagues to support him.”
Former Prime Minister Mrs May refused to say how she voted, but turned up to do so in a glittery, blue ballgown.
Mr Johnson has already received the resignation of his anti-corruption tsar, John Penrose, who said the Prime Minister had breached the ministerial code over the partygate scandal and should quit.
It came as snap polls revealed most of the public think Conservative MPs should have voted to remove Mr Johnson as Prime Minister.
Some 60 per cent of Britons think Mr Johnson should be usurped, according to both a YouGov poll of more than 3,000 people and a separate Savanta ComRes survey carried out on Monday.
A similar proportion of the YouGov respondents (61 per cent) also said they believed the Government did not have the right ideas and policies to deal with the cost-of-living crisis.
Chairman of the committee Sir Graham Brady confirmed on Monday morning he had received the 54 letters from Conservative MPs needed to trigger the ballot.