Rassie Erasmus' side beat the Scots 42-28 in Pretoria to stretch their lead at the summit, although they narrowly missed out on the maximum possible rankings reward.
The world champions needed to win by more than 15 points to collect the full number of ranking points available from the fixture, but had to settle for a slightly smaller boost following their 14-point win.
While the Boks remained firmly positioned at the top, there was movement elsewhere in the rankings.
England climbed back above Scotland into fifth place after hammering Fiji 73-8, just a week after the Scots had moved ahead thanks to their opening-round Nations Championship victory over Argentina.
The top four, however, remains unchanged. The Springboks continue to lead the way, with Ireland second and New Zealand third after both sides recorded convincing victories without gaining any ranking points. The All Blacks cruised past Italy 47-17 in Wellington, while Ireland defeated Japan 36-20.
Further down the standings, Japan moved up to 11th after Wales slipped below them following a defeat to Argentina, who are in seventh.
Spain were the biggest winners of the weekend, climbing four places to 16th after defeating Tonga. Their rise pushed Uruguay, Chile, Samoa and Tonga each down one position.
Latest World Rugby rankings (As of 13/07/2026)
1. South Africa 93.96
2. New Zealand 91.04
3. Ireland 89.32
4. France 87.43 (+0.68)
5. (↑1) England 84.75 (+0.84)
6. (↓1) Scotland 84.09 (-0.02)
7. Argentina 84.06 (+0.29)
8. Australia 80.60 (-0.68)
9. Fiji 78.69 (-0.84)
10. Italy 77.31
11. (↑1) Japan 76.42
12. (↓1) Wales 76.38 (-0.29)
13. Georgia 73.30 (+0.64)
14. USA 69.40
15. Portugal 68.67 (+0.17)
Stars Vusi Moyo, Jaco Williams, Ruben van Heerden, and Carlu Sadie will all make their Test debuts in the Springboks' third Nations Championship fixture against Wales in Durban on Saturday.
It was another big week for Springbok newcomer Quan Horn at Loftus Versfeld on Saturday, as the emerging flyhalf put in another strong performance in the green and gold.
Springbok star Ben-Jason Dixon immediately cast his eye to the challenge awaiting the Boks when they host Wales in Durban next week, predicting they were in for another tense tussle.
A much-changed Springbok team came through a slugfest with Scotland to eventually win 42-28 in their Nations Championship clash at Loftus Versfeld on Saturday.
