These defeats on Wednesday opened the doors for the five sides.
Celebrations will be particularly acute in Malawi and The Gambia as both sides reach the knock-out phase for the first time.
Tunisia will also join the teams in the second round as long as they avoid a defeat by six clear goals to The Gambia on Thursday.
Should the 2004 champions lose by such a scoreline, Comoros – who are currently among the best third-placed sides – could achieve a fairytale qualification.
Two-time champions Ivory Coast are the sole side through from Group E so far and face Algeria in Douala on Thursday in a game the 2019 winners must take three points from to progress.
Sierra Leone and Equatorial Guinea, who meet in Limbe, can also progress from the group.
Three teams can still top Group F, with The Gambia, who have four points, playing Tunisia, who have a point less, while Mali, joint top with the Gambian Scorpions, take on already-eliminated Mauritania.
After the Nations Cup’s group phase comes to a close on Thursday, there are two rest days before the Round of 16 gets underway when Burkina Faso play Gabon on Sunday.
