The IRB has confirmed that referee Alain Rolland erred in not allowing Australia to make a late substitution against South Africa last Saturday.
The Wallabies were forced to play out the closing stages at Loftus Versfeld a man short, although it did not affect the result as the Springboks had all but sewn up a 31-8 victory.
An IRB statement said that, according to Law 3.12 (exception 2), Australia reserve hooker Saia Fainga'a should have been permitted to replace injured hooker Tatafu Polota-Nau.
Touchline microphones picked up Rolland - an experienced referee who officiated at the 2007 World Cup final - telling the Australians that they could not make any more substitutions as they had already used the usual maximum of seven.
"The area of substitution management is a team effort. This was an unfortunate case of human error by the match officials who accept that they made a mistake," said IRB match official selection committee chairman John Jeffrey.
Australian Rugby Union chief John O'Neill said despite the match officials' inaccuracy, no decisions on the night affected the final result of the Test.
"South Africa were absolutely the better side, we congratulate them, they dominated the match, and that is not up for debate at all," he said in Sydney on Thursday.
"However, given the circumstances where the Wallabies were dealing with a massive and mounting injury toll, it was frustrating and unfair for the team to carry additional burdens.
"The challenges they faced at a ground where no Australian team has ever won were difficult enough.
"So I appreciate the IRB acknowledging the match official team failed to recognise Law 3.12 and allow the Wallabies to play out the match with a full complement of 15 players."
Rolland, who will also referee the match between South Africa and New Zealand in Soweto this Saturday, was assisted in Pretoria by Greg Garner of England and Romain Poite of France, with South African Shaun Veldsman the Television Match Official.