Nigeria have climbed up one place to 38th in the updated FIFA world rankings released on Thursday, while South Africa have fallen to 66th in the overall standings.
The Super Eagles' climb takes them sixth in Africa, while Bafana Bafana - who have won their last four matches - are 13th on the continent.
Nigeria's rise takes them above the Czech Republic, and tied with Greece, while they're only one place behind Austria and two off the Netherlands.
Egypt remain Africa's top side, but drop one place to 25th in the overall standings, while Africa Cup of Nations quarterfinalists Democratic Republic of Congo are second in the continent and 28th overall.
Africa's champions Cameroon climb one spot to 35th overall and fifth in the continent, behind Senegal and Tunisia.
Some of Africa's smaller footballing nations have enjoyed rapid climbs, with Namibia (136th), Liberia (133rd) and Ethiopia (120th) moving 20, 17 and 16 places respectively.
However, Burundi, in 132nd, are Africa's big losers, dropping 11 spots.
FIFA World Rankings (CAF)
1. Egypt 2. Democratic Republic of Congo 3. Senegal 4. Tunisia 5. Cameroon 6. Nigeria 7. Burkina Faso 8. Algeria 9. Ghana 10. Ivory Coast