Abdoulaye Diarra scored the winner on 80 minutes after Aliou Dieng had canceled Mohamed Ali Monser first half opener after the break.
It was the first time Tunisia had lost a game in the history of the championship and it came costly as they were booted out of the tournament.
The Carthage Eagles started well and shot into the lead after 14 minutes through CS Sfaxien midfielder Monser who headed home a cross from Saad Bguir past Mali goalie Djigui Diarra.
The Tunisians held on to the lead until the 71st minute when Dieng restored parity by converting a penalty.
The tide suddenly changed the way of the Malians and Diarra sealed victory on 80 minutes curling past Tunisia goalie Rami Jeridi.
Mali will play Cote d’Ivoire for a place at the final on Thursday in Kigali.
Orange Man of the Match
Abdoulaye Diarra (Mali)