Jeremy Corbyn has said he wishes Clive Lewis well and "looks forward to working with him in the future" after he resigned from the shadow cabinet.
Mr Corbyn has told Labour MPs to back the Brexit Bill at its third reading, something Mr Lewis said he could not do.
The Labour leader said: “I would like to thank Clive for his work in the shadow cabinet, which has underlined what an asset he is to the Labour Party and our movement.
“I understand the difficulties MPs representing constituencies which voted Remain have in relation to the European Union Withdrawal Bill. MPs have a duty to represent their constituents as well as their party.
“However, the Labour Party respects the outcome of the EU referendum, so we have asked all Labour MPs to vote for the Bill at its third reading tonight.
“We have been clear from the start that Labour will not frustrate the triggering of Article 50, which represents the start of the process for leaving the EU."
Labour leader Jeremy Corbyn insisted that he has support from MPs on all other campaign issues and upcoming votes.
A total of 52 Labour MP's rebelled against their party leader's three-line whip for a second time to vote against Government's Brexit Bill.
Labour has called on the Government to set out its plans for immigration in post-Brexit UK.