The SNP and other opposition parties at Holyrood voted to refuse legislative consent for the EU Withdrawal Agreement Bill, with just just the Tories backing it. It was rejected by 92 votes to 29.
But the vote is largely symbolic because the Bill is UK legislation and Holyrood cannot back its passage through Westminster.
“This is a sad moment in the history of Scotland and the United Kingdom,” Scottish Government’s Brexit Secretary Mike Russell said.
“It is deeply damaging to the UK as the Scottish Government has set out in detail before.
“But it is particularly bad for Scotland, as all the evidence shows, and it is uniquely offensive to Scottish democracy.”
But Scottish Tory constitutional spokesman Adam Tomkins said the Tories would finally deliver Brexit after securing a majority of MPs at Westminster in last month’s General Election.
“The Bill will pass, the Withdrawal Agreement will take effect and this United Kingdom will at last leave the European Union at the end of this month,” he said.
“Finally it will all be over.”
Labour's Alex Rowley said his party would be backing the Scottish Government in withholding consent for the UK Bill.
He said: "On such a crucial issue as the future of our nation and its relationship with Europe and the rest of the world, Scotland's Parliament and Scotland's Government must have a key role in that negotiation process."
Mr Rowley added: "We also have to be honest and make clear that, while Brexit will now happen, it will not be over with for a very, very long time".