New Zealand were performing the Haka, a traditional pre-match routine involving vigorous movement, stamping of feet and rhythmic shouting, when several mix-ups occurred at Ellis Park in Johannesburg.
"(The mix-ups) occurred as a result of timekeeping challenges and simple human error," SA Rugby chief executive Rian Oberholzer said in a statement.
The closing moments of the Haka clashed with music, fireworks and a flyover by an airliner as a planned schedule went awry.
A sound engineer mistakenly interpreted the cheering of the capacity 62,000 crowd as a sign that the Haka had finished and restarted the music programme.
The Haka, which dates back to the 'Original All Blacks' tour to Europe in 1905, is performed by New Zealand after the national anthems and before the kick-off in each international they play. The
"It was never the intention to schedule any activities that would coincide with such an iconic moment of any Test against the All Blacks," added Oberholzer.
"We hold dear the values and traditions of the game.
"The unfortunate events in no way represent any lack of respect that South African rugby holds for the significance and history of the Haka."
South Africa won the Test 31-27. The two teams will meet again in Cape Town on Saturday.
