The assessment estimates that under the free trade agreement envisaged in the deal, GDP would be 6.1% lower in 11 years time compared to forecasts under continued EU membership.
The analysis also states that the potential for delays to trade and non-tariff barriers, such as country of origin rules and regulatory alignment, could leave food and drink, digital and service sectors particularly vulnerable.
Presenting the new assessment to the Scottish Parliament, Constitutional Relations Secretary Michael Russell told MSPs: “The paper we have published today sets out the impact of this disastrous deal on Scotland. It removes any pretence that the UK intends to seek a future relationship with the EU beyond a limited free trade agreement.
“The Fraser of Allander Institute estimates that Scotland’s economy is already around two per cent smaller - £3 billion - than it would have been without the vote to leave the EU and, let’s be clear, this exit deal does not in any way ‘get Brexit done’. It would merely unleash fresh, ever more complex and ever more acrimonious disputes on the population.
"The likelihood is that it merely postpones a ‘no deal’ crash out for little over a year."
Mr Russell said that by granting Northern Ireland continued access to the Single Market, the deal puts Scottish companies at a competitive disadvantage. He also said that failed to address an expected decline in Scotland's working age population caused by the ending freedom of movement for people.
In an increasingly heated Chamber, with cries of "rubbish" from the Tory seats, Mr Russell said the new Brexit deal was now at the heart of the upcoming election campaign, and added: “The UK Government has repeatedly failed to live up to its promises to fully involve the devolved administrations in the Brexit negotiations. The result is a bad deal which will damage Scotland’s interests and ignores our democratic will.
“The people of Scotland have the right to determine their own future free from Brexit as an independent member of the European Union.”
However Mr Russell's presentation of the impact analysis in Holyrood was branded a "party political broadcast in the most hysterical and ridiculous terms" by Scottish Tory economy spokesman, Murdo Fraser.
Raising the issue with the Presiding Officer Ken McIntosh, he said: "Ministerial statements are to inform Parliament, they should not be used as a 15 minute party political broadcast on behalf of the Scottish National Party. I'm aware we have a general election on its way, but parliamentary must not be abused in this fashion."
Mr McIntosh urged MSPs "not to bring election politics too much into this chamber, please keep election campaigning outside the chamber and keep the chamber for government business."
Scottish Tory constitutional spokesman Adam Tomkins, said he had expected apologies from Mr Russell and Nicola Sturgeon for their previous statements that Boris Johnson would not achieve a deal.
He added: "The truth is Mike Russell called for a transition period. Boris Johnson's new deal provides for one. Mike Russell called for no hard border on the island of Ireland, Boris Johnson's new deal ensures we wont have one. Nicola Sturgeon called for a guarantee on EU citizens' rights and Boris Johnson's new deal provides it.
"Is it not the case the SNP rail against this deal because they want the most chaotic Brexit possible? Is it not the case they want a no-deal Brexit, because the only thing they care about is independence and they think the shortest route to independence is a no-deal Brexit?"
Mr Russell said he had constantly opposed a no-deal Brexit. He added: "I wish to see an end to Brexit and of course Mr Tomkins used to wish to see no Brexit originally, it's a pity he's walked away from that for purely party advantage."
Scottish Liberal Democrat leader Willie Rennie said that it was "incredulous" the Conservative MSPs were defending a deal which "puts a border in the Irish Sea, when they condemned that deal last year."
But he added: "I'm puzzled that the minister states that breaking from the EU will be disaster but breaking from the UK will be of benefit. Does he not get it by now that putting up borders and barriers costs jobs and the economy, that we need to learn the lessons of Brexit, not repeat them with independence?"
Mr Russell said that the Liberal Democrats no longer had a plan to stop Brexit. "His only plan was to have a second referendum and we would still support that referendum, were there a prospect of it succeeding," he said.
He said Mr Rennie had "consistently failed to address the central question", that "because he cannot guarantee in any sense that there would be a defeat for the forces of Brexit now or in the future, there's only one surefire way of getting Brexit finished and moving on as a normal nation, and that is independence."
Scottish Green co-leader Patrick Harvie raised the downgrade of commitments to provide a ‘level playing field’ with Europe in the new Brexit deal. He said: “Liz Truss, the trade secretary, said that scrapping those protections is vital to giving the Tories the freedom and flexibility to strike new trade deals. On the same day an unnamed cabinet source said the level playing field policy ‘has to go’ because ‘it would seriously restrict our ability to deregulate’.“If that Withdrawal Bill is put forward after this general election, we face the very real threat that the Scottish Parliament may be unable to protect Scotland from this kind of hard right extremist ideology. That’s why it’s vital for Scotland to have the right to choose our own future, so we can start to build a progressive, sustainable independent Scotland in Europe."