MPs inflicted the first defeat on the government since 1997
Following the Monday evening vote, a spokesman for Labour Chief Whip Hilary Armstrong - who had sacked the two chairmen - said the government would listen to the will of the Commons.
"We will respond to the will of the House and a new list will be put forward to the parliamentary Labour Party on Wednesday morning and that list will include Donald Anderson and Gwyneth Dunwoody," the spokesman said.
The government had faced widespread criticism after it refused to re-appoint Mr Anderson as chairman of the foreign affairs select committee - reflected in the vote of 301 to 232 to reject the government's proposed alternative membership.
Soon after, MPs also rejected the proposed membership of the new transport select committee, which had included the removal of Labour's Gwyneth Dunwoody as chair, by an even bigger majority of 308 votes to 221.
MPs had been given a free vote on the issue but the outcome will widely be seen as a major humiliation for Prime Minister Tony Blair's re-elected government, this being his first Commons defeat since coming to power in 1997.
Mr Anderson hailed the result as a "great day for parliament" and warned ministers that it would be "very, very unwise" to ignore the new mood among MPs.
"It really is a peasants' revolt and a great day for parliament," he said
And former Labour minister Chris Mullins hailed the outcome of the votes as a "good day for democracy".
"I think it's a boost for parliament over the executive," he said.
Earlier in the Commons, Mrs Dunwoody said she had been "astonished" by her sacking and warned the public would not accept MPs who simply toed the party line.
She said: "What we do on select committees matters because the House of Commons must never become a great morass of people doing what they are told not by the electorate but by the executive."
House of Commons Leader Robin Cook told the House that new proposals for the membership of the foreign affairs and transport committees will be brought forward for MPs to vote on this Thursday.
Decision under review
The committee of selection will review the membership of both committees on Wednesday and draw up new lists with Mrs Dunwoody and Mr Anderson included.
Conservative deputy chairman Nigel Evans said the vote was "a lesson" for the government and "they better think very carefully and make sure that they fully consult with their backbenchers before they try to steamroller anything through that is counter to the wishes of parliament".
After the vote former culture secretary Chris Smith, who had been widely expected to take over the chairmanship of the foreign affairs committee from Mr Anderson, said he was now withdrawing from the list of nominations.
"I have written to John McWilliam [chairman of the committee of selection] to withdraw my name from the nominations for the foreign affairs select committee in order to enable the wishes of the House to be fulfilled," Mr Smith said.