After a goalless draw in 120 minutes, Mali were sharper in penalties winning 5-4 in penalties at the Ahmadou Ahidju Stadium in Yaounde.
Mali had Mamadou Traore and Mouusa Kyabou miss good scoring opportunities earlier in the game.
Meanwhile, Gautrand Ngounimba also came close for the Red Devils of Congo Brazzaville.
After 112 minutes Congo’s substitute Yann Mokombo had a good chance when he dribbled past a defender in the box.
But his clear shot was blocked for a corner.
During the penalties, Congo’s Prince Mouandzu Mapata placed the first penalty out, while all the Mali players converted.
Issaka Samake, Moussa Kyabou, Makan Samabali, Mamadou Doumba and Mamadou Coulibaly all converted penalties for The Eagles of Mali.
Congo on the other hand netted their penalties through Julfin Ondongo, Hardy Binguila, Yann Mokombo and goalkeeper Pavelh Ndzila.
It is the second time Mali’s team get to the semi-final stage of a CHAN tournament after finishing as runner ups in 2016.