The protest, which lasted about six hours, ended after police arrested nine people on suspicion of aggravated trespass. Protesters reportedly swam the River Thames to reach the runway, which is surrounded by water.
The group had erected a tripod and locked themselves together.
The group Black Lives Matter claimed responsibility for the protest on social media. It says expansion consigns the local community of Newham to environmental degradation.
The group says the airport caters to people working in financial services - not the local population affected by its presence.
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Hundreds of passengers were affected. By late morning, 16 flights were cancelled and 12 were delayed.
Among those affected was Casey Collins, a freelance management consultant from Devizes in Wiltshire who was supposed to be on a 7:35 am flight to Luxembourg.
"The problem was that there were only two or three staff there and the queue was about 150 yards long, so it was impossible," he said. "Pretty soon they realised they would have to do a queue-walk to inform everyone. People were behaving themselves. They know it was not the airport's fault, but for a time it was a bit chaotic."
The demonstration was the second in as many months by the anti-racism activists, who blocked traffic leading to Heathrow and held other protests in several British cities.
Last month's protest marked the fifth anniversary of the death of Mark Duggan, a 29-year-old black man shot by London police under disputed circumstances on August 4, 2011.
The killing sparked several nights of rioting in Britain's worst civil disorder in decades.