Jimmy Thoronka, 21, did not return home after the event in the summer of 2014, amid Ebola fears in his home country.
He was arrested after being found sleeping rough in London, but applied to stay in the UK and was offered a scholarship by a London university.
But the Home Office has confirmed his appeal has been rejected.
A spokesman said: “All applications for a visa or leave to remain are considered on their individual merits and in line with the immigration rules.
“Mr Thoronka’s claim did not meet the required thresholds within the immigration rules.”
Almost 4,000 people in Sierra Leone died following the outbreak of Ebola in the country in May 2014.
Mr Thoronka’s adoptive mother was a nurse who contracted Ebola while she was working. She died while Mr Thoronka was competing in Glasgow. She also infected the rest of her family.
Described as Sierra Leone’s top 100m runner, Mr Thoronka competed in one 4x100m relay at the games but did not win any medals.
The sprinter previously said his visa ran out last year and he had not worked or claimed benefits since.
Mr Thoronka was arrested in March this year and warned he faced deportation.
The University of East London (UEL) said it would offer him a place on a foundation degree course if he was granted a visa to stay in the UK.
But a letter from the Home Office informed Mr Thoronka that his claim was “clearly unfounded” and had been refused.
He was told he could only appeal against the decision once he has left the UK.
He told the paper: “What is going to happen to me if I am forced to return to Sierra Leone?
“There is no-one to look after me and support me there and the training facilities are very bad.
“The president of the Athletics Association there said that many of the athletes are just training by themselves, on the tracks at schools which are not very good. I don’t think I will make it if I have to go back.”
The UEL has an established link with athletics – European 200m champion Adam Gemili recently graduated and double Commonwealth Games bronze medallist Bianca Williams is currently studying there.
Cambridge University student Richard Dent, who had never met Mr Thoronka, set up a fundraising page following the athlete’s plight, which has so far raised £31,465.
Mr Thoronka, who has a personal best of 10.58 seconds for the 100m, has previously won medals in African competitions and received the Sports Writers of Sierra Leone’s best male athlete award in 2013.