The vote to reintroduce the employee shareholder proposal as part of the Growth and Infrastructure Bill passed by a margin of 277 to 239.
The controversial Employee Shareholder clause, 27, was originally announced by chancellor George Osborne in last year's Autumn Statement, but was defeated last month in a vote in the House of Lords.
Despite continuous lobbying from employee ownership committees and unions, MPs have chosen to reinstate the clause.
Under the proposals, employers will be able to offer to swap some employments rights, including those relating to redundancy, for at least £2,000 of shares.
Business minister Michael Fallon said the scheme would be "wholly voluntary" and unveiled a concession that he said would ensure that anyone on Jobseeker's Allowance would not be sanctioned for refusing to accept a job offer contingent on participation in the shares-for-rights scheme.
The TUC has said the shares for rights vote "defies logic". Its general secretary Frances O'Grady, said: "This proposal should have been quietly killed off today. It has no support among employers and was heavily defeated in the House of Lords by a wide coalition including prominent Conservative and Liberal Democrat peers."
O'Grady added: "Employment rights should not be for sale. Employers do not want to buy them, and employees will not want to sell them. What is worse is that its only real practical use is as a tax dodge."
Phil Hall, special adviser to ifs ProShare, told HR magazine: "It is deeply regrettable that the Government has again refused to listen to the views of the majority of UK businesses, all of the representative bodies for the share ownership industry and the majority of Peers in the House of Lords."
Sarah Ozanne, employment partner at law firm CMS Cameron McKenna, said: "It's curious just why Osborne is so keen to press ahead with this when the consultation showed only lukewarm support for it, even among employers.
"There may be better support among start-ups but why employees would voluntarily surrender really quite fundamental rights is very unclear."
The Bill will now be returned to the House of Lords on 22 April where peers will one again debate the fate of Clause 27..
