South African national team players were reportedly owed sums in the region of R90 000 each in terms of incentives for recent matches.
The outstanding payments were related to respective Africa Cup of Nations qualifiers and Nelson Mandela Challenge games against Sudan and Mali last year.
South Africa claimed a 1-0 victory over Sudan in the AFCON qualifier at Orlando stadium in November last year.
Acting SAFA CEO Tebogo Motlanthe has confirmed that Bafana players have since been paid their outstanding bonuses.
"The players have now been paid, I just confirmed it now. The payments were made last week Friday," Motlanthe tells snl24.com/kickoff.
SAFA are yet to confirm their new technical sponsorship, believed to be Le Coq Sportif, after the contract with Nike was not renewed.