O'Brien said the gaffe would not have any World Cup consequences for the Irish official who is set to referee the initial All Blacks-Tonga game, while Meuswesen was not involved in the tournament.
However, every referee would be reminded about the scope of video replays and the extent of the referees' and TMO's powers.
"They will be told there should not be any breach of protocol as there was on this occasion.
"They made a call they were not entitled to make. If that means referees miss a knock-on or something else in the leadup to a try, then that's the way it is. This has all been talked about at the IRB level and that was the decision," O'Brien said.
South African Sean Veldsman was the original choice to monitor the television judgments at Nelson Mandela Bay Stadium but he was replaced by schoolteacher Meuswesen who originally hailed from Namibia.
Meuswesen interrupted Clancy's request to check on whether Cowan had grounded the ball after backing up a magnificent break and offload from fullback Israel Dagg.
The TMO's additional inquiry about Dagg's pass changed Clancy's ideas and the pair ruled the try out.
All Black coach Graham Henry supported their ruling even though he knew their verdict had fallen outside their jurisdiction. For some time Henry has campaigned to widen the TMO's powers to check other areas in try-scoring movements.
"If it was a forward pass, it shouldn't have been a try," Henry said.
"If the officials can make good decisions on the evidence they have got, why not? I know it's outside the laws of the game - they should only adjudicate over the goal line. But I haven't got a problem with it.
"That was the reality, it wasn't awarded. I don't know if it was a forward pass or not. I asked Israel Dagg after the game and he reckoned it was 50-50. If we were on the receiving end and South Africa were disallowed a try because it was a forward pass, we would be happy about that."
You have to wonder, though, if the same situation occurred in the final minute of the World Cup final with the All Blacks chasing a deficit, whether Henry would be so magnanimous. His opinion was noble in a test which meant little, the World Cup is something completely different.
The All Blacks missed a clutch of chances to score more tries than Richard Kahui's solitary touchdown. Henry put some of that down to inexperience but this was a side the coach thought would take down the Springboks.
Boks coach Peter de Villiers was jubilant after recent misfires and said it would be a helpful springboard for the World Cup.
* Quade Cooper could assume the kicking duties in the Wallabies' Tri-Nations rugby decider against New Zealand on Saturday if James O'Connor is suspended for disciplinary lapses.
O'Connor failed to attend Australia's World Cup squad announcement last Thursday and will face a code of conduct hearing and could be suspended for the match.
