The man was refused entry after arriving on a flight from Sao Paulo, just two days before the start of the first World Cup finals on the African continent.
On Sunday, police arrested 10 known members of the "Barrabravas" gang who were on the blacklist for the tournament.
Police said the list is made up of people it believes "would commit acts of public disorder, engage in acts of violence and provoke conflict with certain fans of opponent teams."
The men were part of a group of 80 supporters who travelled from South America to Johannesburg through Angola. At least two of the men were Barrabravas leaders and the third was out on bail for murder.
South African police have little experience with massive soccer hooliganism, which has not been a part of domestic games, and have been cooperating with foreign intelligence and police agencies to prevent potential trouble-makers from coming into the country.
South African police minister Nathi Mthethwa said last month local and British police had thwarted an attempt by English hooligans to go to the World Cup via Dubai.
As many as 3,200 English fans known for their loutish and violent behaviour at matches had been told to surrender their passports to prevent them travelling, he said.
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