South Africa lost 2-0 to Sudan in their final group game to miss out on the tournament in Cameroon which will feature 24 nations.
Sudan’s victory sees them finish second, while Bafana failed to qualify in third place.
Percy Tau scored the equalising goal for Bafana Bafana just minutes after the Black Stars' Mohamed Kudus opened the scoring in the second half.
African countries have suffered to varying degrees from the pandemic with South Africa the hardest hit among those south of the Sahara, recording more than 144,000 cases, while Egypt has suffered the worst in North Africa with over 66,000 infections.
CAF’s executive committee will meet in an online conference on Tuesday to decide what to do, and also set out a possible process for completing this season’s two continental club competitions.
Also returning to the national setup after long absences are midfielders Andile Jali, Thabo Matlaba and George Maluleka.
In Bakau, Gambia and Djibouti drew 1-1 for the second time in five days, leaving the countries deadlocked at 2-2 on aggregate.
Stuart Baxter has resigned as the head coach of Bafana Bafana.
The continent’s richest man Aliko Dangote has promised to pay the Super Eagles $50,000 for each goal they score against the Algerians.
Madagascar coach Nicolas Dupuis, whose contract was set to expire at the end of the competition, admitted Tunisia were simply too strong.
Bafana Bafana stunned the hosts Egypt in the last 16 but were eliminated four days later in Cairo after William Troost-Ekong bundled in a late winner for three-time champions Nigeria.
The 30-year-old, who played for Watford before moving to China two years ago, has scored three goals at the African football showpiece in Egypt.
Crystal Palace winger Zaha ensured the Ivorians remained unbeaten against Mali at the tournament as he squeezed home on 76 minutes to book a quarterfinal showdown with Algeria.
The two countries share the 62nd place in the world rankings, suggesting the teams are evenly matched.
From promising to give away phones and cars, to mopping the N2, Bafana Bafana silenced their crtics by beating Egypt 1-0.
Mane broke the deadlock in the 15th minute of a physical game after Senegal pounced on a mistake by Uganda.
The match will be played on Saturday at the Cairo International Stadium.
Bafana Bafana squeezed into the knockout round as the last of the four best third-placed teams in the pool stages having beaten minnows Namibia 1-0.
