Both of these teams can't qualify. Only the top ranked team from each group will qualify. That's why I said that in all probability one of these two teams will miss the ticket to USA. If either Nigeria and South Africa finish at no.2 in their group, then they will get a chance to play the inter-continent playoffs. But out of 9 second placed teams, only one will get a chance to play that match. It is going to be tough. So for both these teams, it is very crucial to finish at the top of the points table. Anyway, personally I will be disappointed in case Nigeria and South Africa lose out. Because I have always regarded them as some of the strongest teams in Africa.
Finishing at the top should be the reason why you go to world cup anyway, we have different results for Europe because football is much much bigger in Europe and usually European or Latin American teams are the winners most of the time, can't remember the last time any team outside of that two continents ever won it to be fair. So when we are talking about African teams, that means the best should go, and second shouldn't, even if you are good, if you are not the best then you shouldn't.
Even one bad day and losing, like just one bad game, still not enough. I am not being ruthless, it's just how football is and if people are not used to it already then they should get used to it without a doubt. I know it will take some for these teams to be as good as European ones, maybe never.