The narrow victory was sealed by Bernard Parker at Soccer City, the stadium at which Spain won the 2010 FIFA World Cup with an extra-time victory over the Netherlands.
The fixture had been expected to lose its status as an 'A' international due to Spain manager Vicente del Bosque making seven changes in the Johannesburg clash.
Six is the most permitted in friendlies, but Del Bosque brought Pepe Reina on for Victor Valdes - after the maximum had been made - as the Barcelona goalkeeper had picked up a calf injury.
FIFA had originally hinted that South Africa could lose ranking points earned by the victory, but the result has been allowed to stand.
A statement from football's governing body read: "FIFA can confirm that the South Africa-Spain friendly match of 19 November 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.
"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 shall be considered as an official match and is therefore included in the November edition of the FIFA/Coca-Cola World Ranking.
"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."
Despite the boost, the additional points were not enough to improve South Africa's place in the rankings of 61st.
