The world football governing body on Monday announced that Bafana Bafana have forfeited the Group C encounter played in March, which they had initially won 2-0, with Likuena earning a 3-0 victory instead.
The decision, which followed an investigation by the FIFA Disciplinary Committee, relegates South Africa to second spot in the group – behind Benin, who are level on points but now boast a superior goal difference – while SAFA are to pay a R216 000 fine.
The national federation have since indicated their intention to appeal the sanction, in line with FIFA regulations, for what they deem an "unprecedented outcome."
"As SAFA, we are deeply disappointed with this unprecedented outcome noting that it was delivered by a single-member panel without reasons, and without affording the Association an opportunity to present legal arguments," read the statement in part.
"The Association confirms that we have requested written reasons for the judgment and intend to lodge a formal appeal with the FIFA Appeals Committee within the prescribed 10-day period under FIFA’s disciplinary rules."
Coach Hugo Broos is set to name his final squad for the two remaining qualifiers against Zimbabwe and Rwanda later this week, with the team set to assemble from Sunday for the matches scheduled for 10 and 14 October respectively.
Bafana will need to win both matches to ensure their tickets to next year's showpiece in USA, Canada and Mexico, should their appeal be unsuccessful.