The Brave Warriors will advance as one of the four best third-placed teams and meet Angola on Saturday for a place in the quarter-finals.
Mali secured top spot in the section with five points, one ahead of South Africa and Namibia, with Tunisia eliminated following another goalless stalemate in the group's other game in Korhogo.
A last-16 tie with Burkina Faso awaits Mali on January 30.
Namibia stunned Tunisia 1-0 in their opening game for the country's first ever AFCON win, but a 4-0 thrashing by neighbours South Africa left them needing a point from their final group match to be sure of a place in the knockout phase.
Prins Tjiueza nearly put Namibia ahead in the 16th minute but his shot was tipped onto the post by Mali goalkeeper Djigui Diarra, who also saved the follow-up effort from Peter Shalulile.
Fousseni Diabate's stinging strike forced a good stop from Namibia's Lloyd Kazapua, with Lassine Sinayoko -- who scored against South Africa and Tunisia -- then heading wide from close range.
In a game of few clear chances, Amadou Dante's late-free kick was turned behind by Kazapua as Namibia held on to join their already-qualified opponents in the next round.
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