The result of 68-55 votes in favour, will mean that from 1 October, only people who have been fully vaccinated against Covid-19 will be allowed into clubs and large-scale events such as concerts and festivals.
In the first major vote since the co-operation agreement between the SNP and the Scottish Greens was finalised, the Greens joined the government in backing the measure to get it passed.
Under Scottish government plans published before the vote, businesses would be legally required to “take all reasonable measures” to ensure compliance.
The scheme will make a QR code available through a smartphone app, which will be scanned before entry is permitted to nightclubs or similar venues, adult entertainment venues, unseated indoor events with more than 500 people, outdoor unseated events with more than 4,000 people or any event with more than 10,000 in attendance.
A dedicated app for the scheme is expected to be available by the end of the month.
It is also hoped that mandating the use of vaccine passports will encourage more reluctant Scots to get vaccinated so they are able to attend.
In England, vaccine passports for nightclubs and other indoor venues will be required at the end of this month, the vaccines minister Nadhim Zahawi confirmed earlier this week.
The Holyrood vote was not to pass legislation, but to pass a motion supporting the implementation of vaccine passports.
Scottish ministers are also considering whether to introduce an offence of “misuse” of the certificates.
Regulations, which will be introduced by the Scottish government, will be reviewed every three weeks, being revoked only when they are deemed no longer necessary.
People under 18, those who are medically exempt, participating in vaccine trials or who are employees at venues will not have to show certification.
Scottish Labour’s health spokeswoman Jackie Baillie said her party supported a certification system based on a negative coronavirus test rather than vaccine status.
She said: “Almost 60,000 people were consulted by the UK government – how many have the Scottish government consulted?
“Have they even spoken to the businesses that will be responsible for implementing this?
“There seems to have been little meaningful engagement, according to the night-time industry and the hospitality industry.”
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