Jordaan beat Mandla "Shoes" Mazibuko for the top spot and would replace outgoing president Kirsten Nematandani.
Jordaan (62) in the run-up to the elections, had spoken about rebuilding South African soccer from "grass roots level" in his bid to restore the image of Safa.
Mazibuko had been a supporter of Orlando Pirates boss Irvin Khoza, who had been considered a powerful candidate for the Safa presidency.
Khoza, however, was ruled ineligible after the disclosure of a resolution in the Safa constitution which prevented a club owner from becoming president of the national body.
Mazibuko was then nominated to oppose Jordaan but the president of the SA Schools Football Association (Sasfa) was unable to garner enough support for the top job.