The majority of Scottish lawmakers - 93 people - cast their ballots against the bill which defines post-Brexit sharing of power between regional authorities.
"I have said time and again it is unacceptable that the legislation gives the UK Government the power to ban the Scottish Parliament from legislating on devolved areas for up to seven years without the Parliament's consent".
The devolved Edinburgh legislature voted by 93 votes to 30 to deny consent for the European Union (Withdrawal) Bill, now going through the national parliament in London, which will cut political, financial and legal ties with the EU.
Despite the speech, the Scottish Parliament passed a motion stating it does not consent to the UK Government's EU Withdrawal Bill. "It would be even more outrageous if, having seen Holyrood specifically refuse consent to this Bill, the Tories imposed it on Scotland against our will", she said.
Despite the vote, Scottish Brexit Minister Mike Russell has vowed this will "not be the end of the process".
But it has never been forced to overrule Holyrood before, and such a move could spark a constitutional crisis.
Theresa May's government has promised that the "vast majority" of the 158 areas where policy in devolved policy areas is decided in Brussels will immediately return to the devolved parliaments after Brexit.
Russell added that agreement could still be reached, however, if the United Kingdom removed the clause from the bill which automatically transfers those new powers to Westminster.
He will call on him come to Scotland and hear "hear the concerns of all parties and to discuss with the Scottish Government and the UK Government any new ideas from any of the parties".
He said: 'This means that the vote on consent for the Withdrawal Bill at Holyrood today need not be the final word on this matter - there is still time to fix this mess'. Welsh finance secretary Mark Drakeford said "this is a deal we can work with which has required compromise on both sides", and the Welsh Assembly is expected to approve the agreement today.
'The blame for that lies entirely with the SNP. The prime minister briefed Conservative backbenchers on Monday about the two options her ministers are considering: a customs partnership which see Britain collecting tariffs on behalf of the EU; and a combination of technological and administrative measures created to diminish friction on a UK-EU customs border.
Scottish First Minister Nicola Sturgeon, leader of the secessionist Scottish National Party (SNP), said Britain was heading into "uncharted constitutional territory". "It's not in Scotland's interests that the SNP prefers picking fights to making a deal".
Lidington has set out details of 24 areas he said would need to come under Westminster control immediately after the United Kingdom leaves the European Union to avoid short-term confusion in areas such as food hygiene, chemicals and animal welfare, which the Scottish Government says is unacceptable.