The 28-year-old - who was born in what was then Sudan but who fled to the United States after 28 members of his family were killed by the Sudanese government - does not have a passport although he does have a green card allowing him to stay in America.
However, with South Sudan not yet having a National Olympic Committee, Marial effectively found himself stateless and unable to compete at the Olympics even though he has run the qualifying time required by the International Association of Athletics Federations (IAAF).
The IOC Executive Board's decision will see him march under the IOC flag at the opening ceremony next Friday along with three athletes from what was the Netherlands Antilles but who refuse to run for the Netherlands since their former country ceased to officially exist in 2010.
"The EB approved a request to allow marathon runner Guor Marial to compete at London 2012 as an Independent Olympic Athlete (IOA) under the Olympic flag," read an IOC statement following the EB decision.
"Marial was born in what is now South Sudan, which does not currently have a recognised National Olympic Committee.
"The athlete, who does not hold a passport from any country, is a permanent resident (refugee status green card) of the United States but not a citizen.
"As such he is unable to compete for the United States, South Sudan or Sudan. Marial qualified for the Games with an A Standard time on 2 October 2011."
Marial's case has been helped by the support of Democratic Senator Jeanne Shaheen from New Hampshire - where he went to school before going to University in Iowa - and will ensure that despite not having a passport he can travel to and back from the Games.
IOC press director Mark Adams said Marial's was to his knowledge a unique case.
"He's lived in the US for 11 years but while he has a green card he has no passport," said Adams.
"I don't think there's been a similar case as to posing the question 'where does this guy come from?.
"He has run some decent times and while they wouldn't be medal times it could well see him in the top 20."
Marial himself had told the New York Times on Friday what it would mean to him to be given the green light.
"It would be great for the people of South Sudan for me to run as an independent," Marial said.
"And the U.S. because that's where I discovered running. It would be great for the whole world."
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