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Five councils, residents, environmental charities and London Mayor Sadiq Khan brought the action after MPs backed the plans in June.
The campaigners said the runway would effectively create a "new airport", having a "severe" impact on Londoners.
But judges rejected the arguments, ruling the plans were lawful.
John Sauven, executive director of Greenpeace UK, said: "This verdict will not reduce the impact on local communities from increased noise and air pollution, nor will it resolve Heathrow Ltd's financial difficulties or the economic weakness in their expansion plans."
Shirley Rodrigues, deputy London mayor for environment and energy, said: "In challenging the decision to expand Heathrow, Sadiq has stood up for Londoners who have serious concerns about the damaging impact it will have.
"We will now consider the judgement and consult with our co-claimants before deciding our next steps."