The SA Football Association (Safa), however, insisted on Wednesday that Bafana was not to blame.
“Normally, the team who have made the transgression is the team that is punished,” Safa’s director of communications Dominic Chimhavi said on Wednesday.
“We abided by all the rules and regulations. As far as we are concerned the result stands. An error by the referee shouldn’t disadvantage and detract from what was an amazing performance and result.”
The controversy started when Victor Valdes limped off the field deep into the second half, having already replaced Real Madrid keeper Iker Casillas at half-time.
Spain had already used their permitted six substitutes but the referee allowed a seventh bringing on Pepe Reina in Valdes’s place.
Bafana coach Gordon Igesund contested the substitution, while Spain’s coach Vicente del Bosque said the decision was supported by South Africa and it was left to the referee’s discretion.
“The six substitutions were made. We asked for the seventh one to the referee table and he [the referee] said it was okay,” Del Bosque said after the game.
“This extra change was a question of fair play and we were very thankful for it.”
Igesund said the unprecedented move should not affect Bafana.
“[Spain] wanted to get their player on, the fourth official and the referee were debating about all this,” Igesund said.
“I think that their players [Spain] thought that I was saying no [to the decision to allow the substitution]. I didn’t say that.
“Obviously it was a language barrier. I said to them quite clearly that the rules were made before the game started.
“They were coming to me and asking me if it was okay to bring the player on.
“I said that I didn’t have a problem with that, I’m not the referee, I don’t control the game.”
Igesund said the decision to allow Reina on to the field was made by the referee, the only person who was able to make such a call.
South Africa — currently ranked 61st in the world and 60 places behind the Spanish side — stand to gain more than 500 points if the result should stand, which could see them rocket up the rankings.