The three-time African champions suffered at the hands of the Blue Sharks on Tuesday but did just enough to advance to the final playoff round
Nigeria played a thrilling 1-1 draw with Cape Verde at the Teslim Balogun Stadium to book their place in next year's FIFA World Cup qualifying playoffs.
Needing just a point to seal the top spot in Group C, the Super Eagles started brilliantly and took the lead after just two minutes, courtesy of Napoli's star man Victor Osimhen.
But Cape Verde fought back impressively to equalise moments later, and the Blue Sharks could have won it late in the game, but Nigeria stood resolute to end the Islanders' World Cup dreams.
The 2013 Afcon kings, therefore, join nine other group leaders, among which only five will qualify to represent the continent at the Qatar 2022 World Cup.
The other qualifiers are Morocco, Egypt, Mali, and Senegal. Tunisia, Congo DR, Ghana, Algeria, and Cameroon complete the set.
The quartet of Morocco, Egypt, Mali, and Senegal had gone through the campaign unbeaten and booked their qualification ticket with a game to spare.
The Atlas Lions won all of their six matches in Group I to outclass Guinea-Bissau, Guinea, and Sudan.
The Pharaohs also won four and drew two games in a Group F with a Pierre-Emerick Aubameyang-inspired Gabon, Libya, and Angola.
Mali's Eagles had little trouble dispatching Uganda, Kenya, and Rwanda to finish as the undisputed leader in Group E.
The Teranga Lions of Senegal won five games, drew one, scored 15 goals, and conceded only four to completely outshine Togo, Namibia, and Congo in Group H.
It was, however, a much closely-fought battle of supremacy in each of the other six groups.
Nigeria had to hold on for dear life as Cape Verde threatened to snatch a late win in Lagos.
Reigning African champions Algeria paraded the best attack in the series, blasting 25 goals in just six games. But they were held 2-2 at home by Burkina Faso, who would have overtaken the Warriors in Group A with just one more goal.
Tunisia finished just two points ahead of Equatorial Guinea in Group B following their 3-1 win over Zambia on Tuesday.
Cameroon's Indomitable Lions knocked Cote d'Ivoire off the peak of Group D after edging their opponents 1-0 courtesy of a Toko Ekambi strike inside the Stade Omnisport Ahmadou Ahidjo in Yaoundé.
The Ivorians needed just a draw to advance but returned home broken-hearted.
It was even more agonising for South Africa, who finished on equal points (14) and equal goal difference (+4) as Ghana in Group G, despite losing 1-0 to the Black Stars at the Cape Coast Sports Stadium on Sunday.
But the Ghanaians progress to the next phase, having scored one more goal than the Bafana Bafana's six.
Congo DR added their name to the playoff draws with a 2-0 victory over the Benin Republic at the Stade des Martyrs de la Pentecôte.
Benin led Group J with ten points heading into that encounter in Kinshasa, but that win catapulted the DRC past the visitors to the summit and into the knockout rounds.
The playoff round is a two-legged, home-and-away format between these ten qualifiers that will see the five aggregate winners seal their place at Qatar 2022.
