Bernard Parker scored the only goal as Gordon Igesund's men recorded a memorable win over the world and European champions, but a seventh substitution by Vicente del Bosque means the match is under threat of being declared void.
Pepe Reina replaced the injured Victor Valdes late on in the encounter after gaining the referee's permission, taking Spain beyond the six-substitution limit for international friendlies.
And FIFA have now confirmed to Perform that, under the letter of the law, the result should not count towards South Africa's official ranking.
"A game between national teams in which one or both of them make more than six substitutions can’t be considered as an A match and, hence, can’t count for FIFA Ranking purposes," said a spokesperson.
However, a defiant spokesman from the South African Football Association disagreed, and believes the scoreline should be allowed to remain.
"As far as we are concerned, the match stands at a category A friendly international and we have not heard of a team being punished for the referee’s transgression," he said.
"(Diego) Maradona admitted to scoring with the hand of God (at the 1986 FIFA World Cup) and I didn’t hear anyone saying England should be awarded the game.
"The referee’s mistake must not disadvantage a team that played the match according to the rules and regulation of an international friendly match."
FIFA are compiling an official report on the fixture, but have removed the result from their official website.
