South Africa failed to qualify for the 2021 Africa Cup of Nations after going down 2-0 to Sudan on Sunday in their final Group C match in Omdurman.
Saifeldin Malik gave the hosts a fifth-minute lead in a clash of former African champions by heading past goalkeeper Ronwen Williams from a free- kick.
Mohammed Abdelrahman doubled the lead on 31 minutes, taking advantage of hesitancy by captain Thulani Hlatshwayo before firing past Williams at his near post.
Elsewhere, Ghana defeated Sao Tome e Principe 3-1 in Accra in a match played at the same time to finish first with 13 points, followed by Sudan (12), South Africa (10) and Sao Tome (0).
Tunisia beat Equatorial Guinea 2-1 in Rades in a match between countries who had already qualified from Group J while Tanzania edged Libya 1-0 in Dar es Salaam in the same section.
Both teams conceded an own-goal in Tunisia after Seifeddine Jaziri raised his goal tally to three from two matches by holding off three Equatoguinean defenders to score in the fourth minute.
Guinea, who secured a place at the 24-team tournament earlier this week, surrendered an unbeaten Group A record when losing 2-1 to Namibia in Windhoek.
Captain Peter Shalulile was the Namibian star, scoring in each half after Mamadou Kane had given Guinea an early lead.
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