The Springboks were grateful for scores from Philip Snyman and Cornal Hendricks in the second half to see them to victory.
However, the All Blacks had the last laugh hours earlier as they won enough ranking points to clinch another HSBC Sevens World Series crown - their 11th title in 14 seasons.
Sam Edgerley's try after the hooter sealed a dramatic 24-21 victory for England against Wales in the third placed play-off.
It looked to be a bleak day for England, who had earlier lost to champions South Africa in the semi-final, as they trailed 21-7 at one point but they hit back to seal a thrilling victory.
There was also joy for France (Shield), Australia (Bowl) and USA (Plate).