Metropolitan Police arrested nine protesters, who made their way onto the runway at around 5.40am and locked themselves together.
The protesters were from the Black Lives Matter UK group, which said the protest was to raise awareness of the UK's environmental impact on black people.
The airport said this afternoon: "Following the protest this morning, the runway has now reopened and the first commercial flight BE1336 to Edinburgh has departed.
“We apologise for any inconvenience caused. Passengers are advised to check with their airline for the latest flight information.”