Wales full-back Hook's 14th-minute strike appeared to go over successfully, but assistant referees Vinny Munro and George Clancy kept their flags down in Wellington.
Hook said later he thought the kick was successful, but the television match official Matt Goddard was not consulted by English referee Wayne Barnes and Wales went on to lose a Pool D thriller 17-16.
The Wales camp, led by coach Warren Gatland, did not make an issue of an incident that ultimately cost Wales dear.
In a statement, tournament organisers said: "Rugby World Cup Limited has clarified the status of the television match official protocol following the Pool D match between South Africa and Wales.
"Under protocol, 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 (International Rugby Board) will not be making further comment."
Wales arrived at their base near Lake Taupo today where they will prepare for next Sunday's critical game against Samoa in Hamilton.
A Wales win would keep them on course for the quarter-finals, but a defeat against a team that beat them during the 1991 and 1999 World Cups could leave Gatland's men staring at a pool stage exit.
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