Jordaan was hoping to follow in the footsteps of Michel Platini and Franz Beckenbauer, former World Cup organisers who have moved to the top seats in football politics, but garnered less than 10 percent of the vote at the Confederation of African Football's congress in Sudan.
Mohamed Raouraoua of Algeria finished first in a hotly contested race for two African places on the all-powerful cabinet of world football with 39 votes and becomes the newest member of the 24-man FIFA committee.
The president of the Algerian Football Federation received 39 votes while Jacques Anouma of Ivory Coast retained his seat with 35 votes, earning another four-year term.
Jordaan, who received widespread praise for his organising of the 2010 World Cup, received just 10 votes in Khartoum. Each of CAF's 53 member countries voted twice.
"Ultimately it is the choice of the national federations of Africa and I can only wish the two winners well," Jordaan told Reuters by telephone.
"There was a lot of fulsome praise for South Africa and the way we organised the World Cup but it didn't translate into votes. We'll need to reflect on it."
Jordaan said he would continue in football administration. He is a vice president of the South African Football Association but has no major role in the game now since he World Cup organising committee shut up shop in January.
"I'll continue my work in football. It's not dependent on a position. There is a lot to do in the country, in the region and on the various committees where I serve," he added.
Jordaan finished behind Suketu Patel of the Seychelles, who received 12 votes but ahead of Nigerian Ibrahim Galadima, who received just five. Kalusha Bwalya of Zambia withdrew from the race in a tactical move that saw him voted instead onto the CAF executive committee, which runs the African game.
The 64-year-old Raouraoua has had two separate terms at the head of Algerian football and has also revived a regional body for north Africa.
He takes the seat of Amos Adamu, who lost an appeal over his suspension earlier this month.
The Nigerian was banned from all soccer-related activity for three years after allegedly offering to sell his vote in the recent World Cup bidding campaign to Sunday Times reporters posing as lobbyists for an American consortium.
