The Springboks will finish the year with a nearly two-point lead over the second-placed All Blacks in the World Rugby rankings.
After South Africa’s 27-26 loss to England at Twickenham, New Zealand had the opportunity to overtake them at the top of the rankings with a win against France.
But Le Bleus’ stunning 40-25 victory in Paris prevented that from happening.
England are third, followed by Ireland (who play Argentina on Sunday) and France.
The Wallabies’ controversial 29-28 defeat to Wales in Cardiff sees them drop from fifth to sixth.
Scotland – who beat Japan 29-20 at Murrayfield – remain seventh, followed by Wales, who climbed one place to No 8 at the expense of Argentina.
Predicted World Rugby rankings after Saturday’s Tests:
1. South Africa 90.61 (-1.22)
2. New Zealand 88.75 (-1.28)
3. England 87.83 (+1.22)
4. Ireland 86.30
5. (↑6) France 85.53 (+1.28)
6. (↓5) Australia 83.92 (-1.17)
7. Scotland 83.05 (+0.28)
8. (↑9) Wales 81.56 (+1.17)
9. (↓8) Argentina 80.81
10. Japan 78.26 (-0.28)