"This is a deeply disappointing result", Shadow Brexit secretary Keir Starmer said.
Despite attempts from Labour, the Liberal Democrats and Scottish National Party to band together in opposition to the bill, May should have the numbers to pass it.
Brexit Secretary David Davis said people did not "vote for confusion" in last year's referendum and Foreign Secretary Boris Johnson urged MPs not to "frustrate" the process.
British lawmakers on Tuesday voted in favor of legislation to sever political, financial and legal ties with the European Union at its second reading, allowing the bill to move to the next stage of the parliamentary process, Reuters reported.
Jeremy Corbyn imposed a three- line whip, ordering Labour MPs to vote against the legislation.
As well as Soubry, former Cabinet Ministers Dominic Grieve and Nicky Morgan have criticised the EU Withdrawal legislation, which will hand the Government unprecedented power to amend laws.
Despite winning the vote on second reading, May is now likely to face pressure to amend the bill before it enters United Kingdom law.
There were five Conservative MPs who did not vote at second reading.
Other Labour rebels will include Leave supporters Kate Hoey, Graham Stringer, John Mann and Frank Field.
The Bill repeals the 1972 Act that took Britain into the European Economic Community and incorporates relevant EU rules and regulations into the domestic law book.
She told HuffPost UK: "We all know that there are Tory MPs anxious about this bill for its blatant assault on our democracy".
The bill, which is created to transfer all existing European law into British law, was voted through by 326 to 290.
Labour MP Stephen Kinnock echoed these comments in the Commons, adding the Bill "seeks to strip Parliament of its sovereign power" and "create a Cabinet of kings".
"As it is, the Withdrawal Bill would see Parliament surrender broad power to Ministers to change laws without proper scrutiny, setting a unsafe precedent".
The Conservative Party formed a minority government and signed a "confidence and supply" agreement with Northern Ireland's Democratic Unionist Party for its ten members to vote with it on key issues.
"And now, the British Government sees fit to introduce legislation that will disempower devolved administrations, centralising power with a cabinet of Brexiteers, free from scrutiny or accountability".