"FIFA can confirm that the South Africa-Spain friendly match ... remains an 'A' international, despite the fact that Spain allegedly used more than the maximum of six substitutes that the laws of the game stipulate can be used for such a match," said FIFA in a statement.
"FIFA have taken into account that both teams had agreed on the conditions of the match and submitted the necessary documentation prior to the match in order for FIFA to confirm it as an 'A' international.
"In this context, South Africa shall not suffer any negative consequences on its part for adhering to the agreed conditions and only using up to a maximum of six substitutes during the match."
The match would also be included in the November edition of the World Ranking, the statement said.
"Regarding the alleged incident of Spain using more than the maximum of six substitutes, FIFA is currently analysing the information at our disposal to assess possible next steps," it added.
Bernard Parker's second-half goal gave South Africa, who have missed out on next's World Cup, a 1-0 win at a half-empty Soccer City in Johannesburg.
Match officials allowed Pepe Reina to come on for injured goalkeeper Victor Valdes after Spain had already made their six permitted changes, much to the chagrin of South Africa coach Gordon Igesund whose protests were waved away.