Goalkeeper Mohamed Zemmamouche could not stop Gabon's last-gasp strike
Hosts Sudan have become the first team to qualify for the ongoing African Nations Championship (CHAN) with a 1-0 victory over Uganda on Tuesday.
Midfielder Mudhather al-Tayeb scored the goal on nine minutes gave the home side a second consecutive win in Group A.
The Nile Crocodiles beat Gabon by the same scoreline in the tournament opener last Friday.
Sudan top the group with six points from two games.
The result also means that Uganda are the first team to be eliminated from the competition after losing the two games they have played.
The Cranes were beaten 2-0 by Algeria in their first game.
In the day's earlier game, Gabon kept alive a slim hope of qualifying for the quarter-finals when salvaging a thrilling 2-2 draw against Algeria.
The North Africans had been leading 2-1 in stoppage time until Ulrich Bembangoye netted a last-gasp equaliser in the Sudanese capital Khartoum.
It was rich reward for the Gabonese who were forced to play the entire second half with only ten men after Remy Ebanega's first-half dismissal.
Gabon, who co-host the 2012 Africa Cup of Nations with Equatorial Guinea, took the lead in the 15th minute through Johan Lengoualama.
They held that lead until the 79th minutes when Algeria's Halil Soudani converted a diving header from Feham Bouazza's cross.
In the 90th minute, Algeria looked to have broken Gabon's resistance as Soudani netted his second head of the match.
But just a minute later, Gabon drew level as Bembangoye profited from a scramble in the box to beat Algeria stopper Mohamed Zemmamouche for an unlikely equaliser.
Algeria are second in the group with four points while Gabon has one.
The final games in the group will be played on Sunday with Gabon facing Uganda while Sudan take on Algeria.
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