The majority of Scottish lawmakers - 93 people - cast their ballots against the bill which defines post-Brexit sharing of power between regional authorities.
He added the Tories' "shambolic handling" of matters meant the issue could be resolved in the Supreme Court - where judges will rule if the Scottish Government's alternative Continuity Bill falls within Holyrood's legislative competence.
If no deal between Edinburgh and London can be reached, Westminster has the option of introducing the Withdrawal Bill against the wishes of the Scottish Parliament - but it has never been forced to overrule Holyrood before.
"That is why I must recommend the Scottish Parliament votes against accepting the bill in its current form".
Scottish Brexit Minister Michael Russell said he hoped May's team would accept his proposed solution of amending the clause allowing the U.K.to change European Union laws affecting Scotland, and said the U.K government needed to show more flexibility in future talks.
"We are likely to be joined by Labour and the Liberals and the Greens in the Scottish Parliament so it will only be the Conservatives that vote to go ahead", she said. The party maintains that the bill remained a power-grab.
Sturgeon, the first minister and SNP leader, has decided that consultation is not enough, and insists that her government or Holyrood should be given the legal power to block any changes they disagree with. 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. "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.
A source said: "It's a nonsense to pretend that the Scottish position is defending devolution".
Scotland's parliament is expected to formally reject legislation for taking Britain out of the European Union on Tuesday in an unprecedented move that would set the scene for a constitutional crisis. On that occasion the UK Government responded by removing those parts of the Bill. United Kingdom ministers have rejected this stance as an unacceptable veto.
Ahead of the debate, a report from the assembly's external affairs committee said its six objectives for improving the bill had still not been met in full, despite the progress made.