The money was allegedly paid to former FIFA members Jack Warner and Chuck Blazer. A separate cash payment in US$10,000 stacks was collected from a hotel room in Paris from a high-ranking South African bid committee official.
The indictment claims Warner was offered over $1 million dollars by South Africa's rival bid, Morocco, but Blazer "learned from Jack Warner that high-ranking officials of FIFA, the South African government, and the South African bid committee, were prepared to arrange for the government of South Africa to pay $12.9 million to 'support the African diaspora'.
Blazer "understood the offer to be in exchange for World Cup votes" but later "learned that the South Africans were unable to arrange for the payment to be made directly from government funds". Blazer was to personally benefit to the tune of more than$1 million.
The indictment adds: "Arrangements were thereafter made with FIFA officials to instead have the $12.9 million sent from FIFA - using funds that would otherwise have gone from FIFA to South Africa to support the World Cup - to CFU (Caribbean Football Union).
"In fact, on January 2, 2008, January 31, 2008 and March 7, 2008, a high-ranking FIFA official caused payments...totalling $10 million - to be wired from a FIFA account in Switzerland to a Bank of America correspondent account in New York ... controlled by Jack Warner."
Blazer was paid $970,000 by Warner but never received the full amount he had been promised.
Blazer has pleaded guilty to 10 criminal charges, while Warner has denied any wrongdoing.
South Africa has dismissed as "baseless" the allegations made Wednesday in a US indictment that the country paid millions in bribes to host the 2010 World Cup.
"We are disappointed at the baseless and untested allegations and request proof from anyone who has contrary evidence," national football association spokesman Dominic Chimhavi said.
"Our bid campaign was run by, among others, late president Nelson Mandela, former president Thabo Mbeki and several government ministers, who are men of integrity."