Two-times champions the Springboks were beaten 34-32 by the Brave Blossoms in Brighton on Saturday, with Karne Hesketh going over in the corner with the final play of the match.
And South Africa are already seeing the adverse effects of that defeat, slipping below England (3rd), Wales (4th) and Ireland (5th), making them the biggest fallers in the latest edition of the rankings.
The All Blacks remain the top-ranked team while the Wallabies hold second position.
Japan, meanwhile, climb two places to 11th, but it is Georgia who experience the biggest rankings boost.
Georgia picked up an impressive 17-10 win against Tonga just hours before Japan's shock triumph and rise to 13th from 16th.
Tonga, meanwhile, slip to 14th.