The Lesotho FA are delighted with the ruling that saw Bafana docked three points for fielding an ineligible player in their World Cup qualifier held in March.
South Africa secured a 2-0 win in that game, but have now seen their points for that game subtracted from their tally, with Lesotho handed a 3-0 win.
The country was found to have broken FIFA rules for fielding the suspended Teboho Mokoena.
The outcome means that South Africa drops to second place in Group C with 14 points from eight games, behind leaders Benin on goal difference, with two games to play.
Lesotho, meanwhile, moved on to nine points in fifth place on the six-team group.
LEFA secretary Mokhosi Mohapi told the Sowetan: ‘FIFA has done well to respect its own regulations.
“We had always maintained that our pursuit of this case had nothing to do with South Africa. Lesotho is a bona fide member of FIFA, and we played the rightful role to ensure the football rules are respected. We are happy to have been vindicated.”
Bafana still have a chance to qualify as they face already-eliminated Zimbabwe and fourth-placed Rwanda in games next month.
Mohapi added: “If Bafana eventually make it as the group winners, I will buy their shirt and support them at the World Cup because they would have earned their place. Mr [Hugo] Broos should know I was not talking nonsense when I said SA has a case to answer. I now feel fulfilled.”