Sierra Leone shocked everyone by coming back to draw 4-4 against the Super Eagles whilst Egypt, struggling, got dealt a massive blow with Mo Salah testing positive for COVID.
Nigeria appeared to have three 2021 qualifying points in the bag when they built a four-goal lead after 31 minutes in Benin City against opponents 88 places below them in the world rankings.
But a sensational fightback that began just before halftime as Kwame Quee scored reached a climax five minutes from time when Al-Hadji Kamara equalised.
Bafana Bafana needed a goal from Rangers midfielder, Bongani Zungu, on 90 minutes at Moses Mabhida to seal a tired 2-0 win over Sao Tome e Principe despite 110 places dividing them in the world rankings.
Percy Tau put Bafana ahead on 55 minutes from the penalty spot after he was fouled and Zungu nodded a corner past substitute goalkeeper Nilson Taty.
It was another unimpressive showing by South Africa under coach Molefi Ntseki, who has achieved just three victories in six Cup of Nations and friendly international outings.