Michael Matheson will be barred from Holyrood from tomorrow for 27 sitting days and lose his salary for 54 calendar days after MSPs backed a motion to impose the sanctions.

The suspension takes effect from Thursday, after 64 opposition MSPs voted to back the recommendations of the Standards Procedures and Public Appointments Committee, while none voted against and 63 SNP MSPs abstained.

An SNP amendment which chided Tory member of the committee Annie Wells for comments she made about Mr Matheson before she voted on the issue was passed by 68 votes to 56 with two abstentions.

The amendment also called for an “independent review” of the complaints process in Holyrood.

The SNP successfully amended the motion to include complaints about the process, before then abstaining from voting on the final amended version.

In scenes Scottish Tory leader Douglas Ross said were “bizarre in the extreme”, the SNP voted for the amendment, but then abstained when it came to voting on the amended motion.

First Minister John Swinney last week robustly defended Mr Matheson, and said he did “not believe that the sanction can be applied” because of comments made by Conservative member of the committee Annie Wells that recommended the sanction.

Mr Swinney said last Thursday the findings as “prejudiced” and claimed that Ms Wells had tainted the process through statements she made last year, describing Mr Matheson’s explanation as being “riddled with lies”.

But the Scottish Greens effectively scuppered any chance that Mr Swinney had of winning a vote against the punishment after the SNP’s former coalition partners said they would back it in full.

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During an angry debate ahead of the vote this afternoon Mr Ross accused Mr Matheson of a “deliberate and shameless attempt to pull the wool over the eyes of this Parliament”.

He said: “This is not a harmless mistake that some have attempted to present.

“This was a deliberate and shameless attempt to pull the wool over the eyes of this Parliament and the public.

“It is an open and shut case.”

He also accused Mr Swinney of engaging in “bully boy” tactics that would “make Donald Trump blush”.

“I want to put on record that the actions of John Swinney, the actions of the First Minister, towards my colleague Annie Wells, would make Donald Trump blush,” he said.

“It is disgusting and disgraceful behaviour that demeans the office of First Minister because he has targeted members of an independent committee in this Parliament and is attempting to undermine due process with his bully boy tactics.”

Scottish Labour deputy leader Jackie Baillie said it is the “cover up rather than the original sin” which was “always the problem” in the Matheson scandal.

“It is the cover up rather than the original sin that is always the problem," she said.

“And it is the contempt of his actions for Parliament, for the press and the public that I am most disappointed by.

“It is a profound error of judgment from someone who I have always had a great deal of respect for.”

Tory MSP Stephen Kerr accused the Scottish Government of a “vindictive” attack on Ms Wells.

The Conservative MSP found herself at the centre of a storm over comments she made relating to Mr Matheson before a committee on which she sat recommended his suspension.

Intervening during a speech by Kate Forbes, Mr Kerr – who recused himself from the same committee earlier this year claiming he would not be able to be impartial – said: “This amendment is nothing but an attack on the integrity of a member of this Parliament.”

He added: “With what Kate Forbes has been through over the last year does she not recognise that this is an attack on an honourable member and is motivated by vindictive purposes?”

Ms Forbes stressed that her remarks related to the principle of the issue rather than Ms Wells and went on to urge the Scottish Parliamentary Corporate Body to review the complaints process in Holyrood to “restore integrity in confidence”.

She said MSPs should engage with concerns about the process which led to the recommendation of sanctions.

“To dismiss them now will have serious consequences for members who, in the future, may themselves be the subject of the committee’s investigation,” she said.

“There’s a fundamental principle of natural justice at stake here.”

Mr Matheson is to be barred from all proceedings in the chamber and committees, but not from the parliamentary estate.

He will not be able to return to proceedings until early September after MSPs return from summer recess.

An investigation by the Holyrood authorities, which reported in March,  found that he breached the code of conduct for MSPs by racking up a near-£11,000 data roaming bill on his parliamentary iPad while on holiday in Morocco, which he later said was caused by his children watching football. He previously said that the recommended sanctions were “excessive” and “unfair” but that he would accept parliament’s decision.

Following his suspension, Mr Matheson apologised but added that he looked forward to “continuing to represent the people of Falkirk West, as I have done for many years”.

In a statement released in the minutes after the vote, Mr Matheson said: “I apologise and regret that this situation occurred. I acknowledge and accept the decision of Parliament.

“I also note that Parliament has called for the Scottish Parliament Corporate Body to carry out an independent review of the Parliament’s complaints process to restore integrity and confidence in the Parliament and its procedures, which I hope will be progressed.

“I look forward to continuing to represent the people of Falkirk West, as I have done for many years.”

Speaking to reporters in Holyrood, Mr Swinney said Mr Matheson’s suspension was not “part of his campaign plan” when asked if it had been a tough start to the General Election for the SNP.

But the First Minister said he did not think the former health secretary should resign as an MSP, telling journalists in Holyrood: “He made a mistake and has been given a punishment by Parliament which I accept unreservedly.

“Michael should accept that punishment and continue to serve the people that sent him here.”

He added: “Parliament has accepted this is appropriate and I accept what Parliament has said.”

Asked if he thought it was a difficult start to his party’s General Election campaign, he said: “You just have to play the ball as it lands. This wasn’t part of my campaign plan. But the issue has arisen and I have as First Minister and leader of the SNP, I have to deal with what emerges in front of me.

“I wouldn’t be the person I am if I just said ‘Ok, let’s have a flawed process. Let’s turn a blind eye. That’s not John Swinney and I’m not going to start doing that now.”

As well as the vote on the standards committee’s recommendations, a second motion pushed by the Scottish Conservatives took place later on Wednesday calling for Mr Matheson’s resignation as an MSP.

MSPs later voted to reject calls for Mr Matheson to resign.

They voted by 68 votes to 55 against the move, instead passing a Green amendment which removed the most of the Tory motion and called for reform of the process for considering sanctions for MSPs as well as another from Scottish Labour calling for a process to recall MSPs.

During the second debate Mr Ross said that while Mr Matheson is to receive a suspension and a loss of wages, “any other Scot would have been handed their P45 straight away”.

He said: “If someone is found to have falsely claimed £11,000 from their employer, in this case the taxpayer, then they lied about it as part of a cover-up, they would have been sacked.”

He insisted the former health secretary’s actions were not a “harmless mistake”, saying he had made a “deliberate and shameless attempt to pull the wool over the eyes of this Parliament and the public”.