The debate was tabled by Conservative transport minster Theresa Villiers on 'opposition day', but both the Liberal Democrats and several Labour MPs voted with the motion.
Transport secretary Geoff Hoon last week confirmed the government's intention to build a third runway at Heathrow.
The decision has proved divisive, with Labour MP Andrew Slaughter resigning last week, and then a second MP Virendra Sharma quit immediately after the vote. Both MPs have constituencies in west London that would be directly affected by a third runway.
Government arm-twisting ensured a Labour win. While 50 MPs had earlier signed an 'early day motion', signalling the intention to vote against the third runway, only 28 went on to do so.
The Conservative motion read:
"That this House urges the Government to rethink its plans for a third runway at Heathrow Airport and to give full consideration to alternative solutions; regrets the Government’s heavy reliance on data supplied by BAA in assessing the case for expansion and notes the likely forthcoming break-up of BAA’s ownership of three of 5 London’s airports following the investigation by the Competition Commission; believes that the consultation paper Adding Capacity at Heathrow Airport was deeply flawed, as it paid insufficient regard to the costs of air and noise pollution in the surrounding areas and the commitment to curb carbon dioxide emissions to tackle climate change; regrets the fact that provisions to improve high-speed rail lines from 10 Heathrow to major cities have not been fully explored, along with the potential of other UK airports to handle more long-haul flights; and urges the Government to initiate a consultation on a new national planning policy statement on the theme of airports and high-speed rail."