Ali Badra Sylla scored the only goal of the game in the evening kickoff when he headed home from a fine Mamaye Coulibaly cross to give Mali the lead in the fourth minute.
While both sides had chances to extend the lead, the Eagles held firm to progress to the final four, where they will meet hosts Senegal on Wednesday following the Teranga Lions’ victory over Benin.
Ghana and the Ivory Coast will clash in the other semi-final on Tuesday after defeating Burkina Faso and Togo to advance.
In this year’s Wafu Cup, the eight First Round losers drop into the plate competition, offering a secondary route to silverware.
Liberia advanced to the final four in Sunday’s early kickoff when the outstanding Kelvin Potis scored the only goal of the game in the 26th minute.
Niger had earlier been victims of the biggest controversy of the tournament so far, when forward Idrissa Halidou was brought down by goalkeeper Alpha Jalloh, but the ball fell to a Nigerien forward to finished with aplomb.
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However, the referee opted to bring back the game and award a penalty, with Jalloh saving Halidou’s weak effort.
Liberia now progress to meet Guinea, while The Gambia will face Cape Verde—Nigeria’s vanquishers—in the plate semi-finals.