Previously known as the Great Repeal Bill, the EU Withdrawal Bill will convert all existing EU laws into United Kingdom law.
In a statement, Prime Minister Theresa May said that parliament had taken a "historic" decision.
Her government has warned that voting against the Bill would result in the United Kingdom suffering a "chaotic" European Union exit. Brexit secretary David Davis said the position paper would highlight Britain's desire to use its assets and capabilities in partnership with the EU.
The legislation would repeal the 1972 European Communities Act and convert directly-applicable EU laws and regulations into United Kingdom law.
Labour and trade unions also fear ministers may seek to change EU regulations on the environment and workers' rights as they transfer them into United Kingdom law.
Most likely to be revised are the government's plans to use so-called Henry VIII clauses - which date back to the executive orders used by the Tudor monarch - to table between 800 and 1,000 pieces of secondary law, on top of the over 20,000 European Union regulations, directives and United Kingdom laws now in place.
She said: "My worry is we've boxed ourselves in here despite some very legitimate things Keir Starmer is saying about changes needed to this bill".
Speaking to Sky News, shadow Brexit minister Jenny Chapman said: "Labour will not block Brexit".
He said: "She and I both voted to implement Article 50 and that means respecting the result of the referendum".
A total of seven Labour MPs however rebelled against the party line and backed the bill.
Having lost her majority in the Commons in June's election, May is vulnerable to rebellions from her own side. Several Conservatives said that on this basis they would back the bill at this point. She will join Labour MP Kate Hoey who will also back the government in the vote, expected at midnight.
Such a process would take the raw politics out of the debate and help reassure legislators that the government is being true to their word concerning the use of such powers.
In Nottinghamshire Conservative Broxtowe MP Anna Soubry has already voiced dissent by asking the Prime Minster to allay fears the process could become an "unnecessary government power grab".
However, of one thing I am clear: the Labour Party's decision to oppose the Bill at Second Reading is transparently about tactical positioning and not in the public interest. "A significant number walked hand in hand with the Tories and have given the Government extreme powers not seen since the Middle Ages".
He also lashed out at Sinn Féin for its policy of not taking up seats in Westminster warning that the vote will "again reflect the absence of the voice of Irish nationalism from Westminster". "The British people didn't vote for confusion and neither should Parliament". "We can not give them these vast powers", warned Goodman.
The party announced last month it favoured continued membership of the single market and customs union during a transition period lasting as long as four years after the formal Brexit date of March 2019.