Linesmen ruled the 14th-minute attempt by Hook, which would have narrowed South Africa's early lead in the Pool D match on Sunday to 7-6, passed outside the righthand upright. Wales fullback Hook was among many at the match or watching on television around the world who thought the kick was successful.
"I was running back because obviously I thought it was over," Hook said. "If there was any doubt I would have stayed there and watched it go over.
"Wayne Barnes was in the same position as me. He obviously didn't give it and I thought it was over so I thought that (to ask the television match official) would be the best thing to do. Obviously not."
England's Barnes accepted the decision of the linesmen, George Clancy of Ireland and Venny Munro of New Zealand, and did not call for the kick to be reviewed by the television match official.
The IRB said in a statement Monday that "the referee may consult the assistant referees or the Television Match Official if he is unsure as to whether a penalty kick, drop goal or conversion has been successful."
"During the match in question, the match official team felt at the time that there was no need to consult the TMO following a Wales penalty kick as they were confident that the kick was not successful. Correct protocol was therefore followed."
The IRB said it would make no further comment.
Wales coach Warren Gatland was not critical after the match of the linesmen's decision.
"I thought that kick in the first half might have been pretty close," he said. Springboks fullback "Francois Steyn said at halftime in the tunnel that he thought it went over. Those are the things that happen in sport."