Despite their narrow 27-26 loss to England on Saturday, the Springboks will end 2021 ranked as the No 1 team in the world.
That loss at Twickenham was offset by the fact that New Zealand, the second-ranked side going into the final round of internationals and who could have overtaken South Africa, were stunned 40-25 by France in Paris.
That leaves the Springboks with almost a two-point lead over their traditional rivals and rounds off a year in which they beat the British and Irish Lions, ended third in the Rugby Championship and won two out of three on their northern hemisphere sojourn in November.
England remains third, less than a point behind the All Blacks while Ireland are fourth.
France have moved to fifth after their win while Australia drop to sixth after losing 29-28 to Wales at Cardiff Arms Park.
The rankings are officially released later this week
Latest World Rugby rankings
1. South Africa 90.61
2. New Zealand 88.75
3. England 87.83
4. Ireland 86.30
5 France 85.53
6 Australia 83.92
7. Scotland 83.05
8. Wales 81.56
9. Argentina 80.81
10. Japan 78.26