The Scottish Greens voted against the motion, with party co-leader Patrick Harvie branding it “chaos for the sake of chaos”.
If it had passed, all ministers in the minority SNP government would have been forced to quit.
Opening the debate, Scottish Labour leader Anas Sarwar thanked Mr Yousaf for his service and wished him well, but said Scotland was “crying out for change” from the UK Conservative government and the SNP Scottish government.
He said the country needed “credible and effective leadership” to deal with “twin crises” in the economy and NHS.
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Mr Sarwar added: “I have no confidence in the SNP’s ability to deliver that and that is why I am bringing this motion to parliament today.”
The outgoing first minister defended his government’s record, adding that in the 13 months he has spent in charge he had not “heard a single positive idea” from Scottish Labour.
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Mr Yousaf added: “What I have heard is the deafening sound of principle after principle being thrown out of Anas Sarwar’s window.
“U-turning on the two-child cap, U-turning on the devolution of employment law, U-turning on the devolution of drug law, U-turning on his support for Waspi women.”
Mr Yousaf said pro-UK parties, in their “cosy Westminster alliance”, would be “terrified” of a vote of no confidence.
He added: “As I have found out only too well in the last few days, politics is definitely about the choices we choose to make.
“As a government, I am exceptionally proud of our choices.”
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Within hours of the powersharing deal with the Scottish Greens coming to an end last week, Scottish Tory leader Douglas Ross announced he would be bringing a motion of no confidence in the first minister.
Angry over the way the party was dumped from government, the Scottish Greens announced its MSPs would be backing the motion.
Scottish Labour then announced it was planning a motion of no confidence in the Scottish government.
Mr Yousaf reached out to his political opponents in an effort to stem the uprising but conceded that he had “underestimated the level of hurt and upset” his actions had caused Scottish Green colleagues.
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The Scottish Tories dropped their motion following Mr Yousaf’s resignation, but Scottish Labour pressed on as the party believes the decision on the next first minister should be put to the public.
Mr Yousaf intends to remain in post until his successor is announced.
Former deputy first minister John Swinney and ex-finance secretary Kate Forbes have emerged as potential frontrunners to throw their hat into the ring.
Mr Sarwar pointed to reports that Ms Forbes could struggle to appoint ministers and described Mr Swinney as “the finance secretary that broke the public finances and the worst education secretary in the history of the Scottish parliament”.
Mr Ross, whose party threw its support behind the Scottish Labour motion, was forced to apologise to Mr Swinney after referring to him as “not so honest John” in the Holyrood chamber.
Mr Ross was first reprimanded for referring to Mr Swinney as “honest John”, but when presiding officer Alison Johnstone reminded him not to use nicknames, he said: “Oh sorry, I thought it was on accuracy because it would be not so honest John with some of the things we’ve heard recently.”
Apologising, Mr Ross said: “I will apologise. I’m very sorry for any hurt caused.”
The Scottish Tory leader added: “Whether we have a bitter battle or a cosy coronation to elect the next leader of the SNP, they will continue campaigning for independence and the Scottish people will continue to be failed by them.”
Thousands of farmers from across the UK are expected to gather outside Downing Street today – in the biggest protest yet against the government’s changes to inheritance tax rules.
The reforms, announced in last month’s budget, will mean farms worth over £1m will be subject to 20% inheritance tax from April 2026.
Farmers say that will lead to land being sold to pay the tax bill, impact food security and the future of British farming.
The Government insists it is “committed” to the farming industry but has had to make “difficult decisions”.
Farmers from Scotland, Northern Ireland, Wales and England will arrive in London to hear speeches from agricultural leaders.
Sky News understands TV presenter and farm owner Jeremy Clarkson, Conservative Party leader Kemi Badenoch and Lib Dem leader Ed Davey will also address crowds.
Protestors will then march around Parliament Square.
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‘It’s really worrying’
“It’s unfortunate, as Labour had originally said they would support farmers,” said fourth-generation farmer Will Weaver, who is attending today’s rally.
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His 500-acre cow and sheep farm in South Gloucestershire has been in his family since 1939.
“We’ve probably buried our head in the sand a little bit. I think, back of a fag-packet rough estimates, tax is going to be north of half a million [pounds].”
The government is keen to stress that farmers will get a decade to pay the bill – but that comes as little comfort to Will: “It’s more than our profit in any year that we’ve had in the last 10 years. Dad’s saying we’ll have to sell something. I don’t know if we’ll be able to raise that sort of money through a mortgage. It’s really worrying.”
The Treasury says only the wealthiest estates, around 500 of them, will have to pay under the new rules – claiming 72% of farms won’t be impacted.
But farmers say that calculation is incorrect – citing that DEFRA’s own figures show 66% of farms are valued at over £1m and that the government has undervalued many estates.
At the same time as the rally, the NFU is addressing 1,800 of its members in Westminster before they lobby MPs.
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2:28
The president of the National Farmers’ Union says farmers are feeling
‘Understanding has been betrayed’
Max Sealy represents the NFU Dairy Board in the South of England.
“We have a detailed job to do to explain why this is wrong not just for farming, not just for the countryside and not just for our families, but for the economy in general,” he said.
“This is a bad tax – it’s been badly implemented because it will affect growth productivity in the country.”
He told Sky News Labour made promises to farmers ahead of the election.
“Both Steve Reed and Keir Starmer came to our conference two years ago and told us farming wasn’t a business like any others and that he understood the long-term nature of farming – that understanding has been betrayed,” he said.
In a joint statement, Chancellor Rachel Reeves and Secretary of State for Environment, Food and Rural Affairs Steve Reed said: “Farmers are the backbone of Britain, and we recognise the strength of feeling expressed by farming and rural communities in recent weeks. We are steadfast in our commitment to Britain’s farming industry because food security is national security.
“It’s why we are investing £5bn into farming over the next two years – the largest amount ever directed towards sustainable food production, rural economic growth and nature’s recovery in our country’s history.
“But with public services crumbling and a £22bn fiscal hole that this Government inherited, we have taken difficult decisions.
“The reforms to Agricultural Property Relief ensure that wealthier estates and the most valuable farms pay their fair share to invest in our schools and health services that farmers and families in rural communities rely on.”
A Met Police spokesperson said it was “well prepared” for the protest and would have officers deployed to ensure it passes off “safely, lawfully and in a way that prevents serious disruption”.