Holyrood voted 66 to 28 in favour of a People’s Vote after it was put forward in a Liberal Democrat amendment to a government motion during a chamber debate on the Brexit threat to international scientific research in Scotland.
The SNP and Greens backed the Lib Dems in the face of Conservative opposition and 21 MSPs abstained.
Liberal Democrat MSP Tavish Scott, who tabled the motion, highlighted many in Scotland’s higher education sector want a right to vote, including the 23 senior figures from Aberdeen, Edinburgh and St Andrews universities who signed an open letter warning of the consequences of Brexit and calling for a People’s Vote.
He said: “There appears no obvious upside to dragging the UK and Scotland’s higher education sector out of the EU, that is why so many in this sector want a right to vote on whatever cobbled-up negotiation appears out of London and Brussels.
“This Parliament should speak for our university and research sector, and all the people who work in it, and we should give them a right to a vote on it in the future.”
Higher education minister Richard Lochhead said he had heard of higher education staff being “left in tears” and considering leaving the UK over Brexit, and about universities hiring immigration lawyers.
He said: “In Scotland, a country that voted overwhelmingly to remain in the EU, we should be resolutely focused on attracting the best minds in Europe to work and study here to help us build a successful, prosperous nation, but instead, thanks to the actions of others, we face the prospect of a Brexit brain drain.
“We have to stand together and stop that happening.”
Scottish Green education spokesman Ross Green added: “We’re fast running out of time but here is a window in which we can avoid this nonsense and reverse the damage already done. I hope we can seize it.”
Labour’s Iain Gray said Brexit has been a “chaotic and catastrophic process”, and urged the final deal must achieve as “close a relationship as possible with the EU”.
Conservative MSP Oliver Mundell accused the Lib Dems of having a “somewhat obsessive wish to hold another referendum”.
“We believe that this matter has already been settled and that the best Brexit deal will now be secured by ensuring co-operation across all the parties with everyone doing what they can to support the prime minister as she seeks to build a consensus,” he added.
“The fundamental climate in which our country operates internationally is going to change, but we have to remember that at the end of the day, that’s what the British people as a majority voted for and the job of the UK Government is to try and balance out those different priorities.”