The Kiwis were crowned overall Series champions with a 42-10 victory over Argentina in the quarter-finals before beating Wales 26-14 in the semis.
But a 28-21 loss to the Springboks in the final soured the overall triumph, as South Africa came from 14-7 down at half-time to blitz the Kiwis in the second period.
"I think looking back at the season we had our highs and our lows, but it is just good for us to come back and finish the season on a high," South Africa coach Paul Treu said.
"We had some bad moments, but those bad moments were needed to make up for our results towards the end of the season and to give credit to our guys and those back home for having the faith and the belief in the team that we could stay the distance."
South Africa’s run to the final included a 24-17 semi win over England, who beat Wales 24-21 in a thrilling contest for third place.
The USA, meanwhile, won their second Plate in a row with a 17-7 defeat of Argentina.
Australia beat Kenya 12-5 for the Bowl, while France edged Russia to the Shield with a 21-17 win.
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- South Africa