In a controversial end to the second half, whistler Janny Sikazwe initially drew the match to a close with five minutes still on the regulation clock.
The game was restarted before the Zambian official again blew for time up in the 89th minute, and before any additional time for several stoppages including substititions, VAR checks and two penalty kicks had been accounted for.
The teams left the pitch amid considerable Tunisian anger only to be requested back later to resume the closing stages.
Mali coach Mohamed Magassouba was digesting the win in his press conference when it was interrupted by tournament officials who declared the remaining time must be played, however, Tunisia failed to reappear and Mali were declared winners.
Tunisia coach Mondher Kebaier called the referee's actions "inexplicable", adding: "He blew for full time and asked us to go to the dressing room, so the players were in their ice baths and then he asked us to come back out.
"In 30 years in this business, I have never seen anything like it."
Former Rangers loanee Lassana Coulibaly was among the Mali substitutes and the midfielder was introduced on 81 minutes amidst the turbulent closing stages with his team leading 1-0.
Moments before, with 77 minutes on the clock, Tunisia had been given a penalty lifeline through a VAR review, but Wahbi Khazri missed his chance to level the scores and Ibrahima Kone’s 48th minute spot-kick remained the difference between the sides.
A late red card was also shown to Mali's El Bilal Toure. VAR questioned the decision but it was not overturned by the referee who then ended the game early a few seconds later prompting Tunisian protestations and a security escort for the officials.
"It is a difficult situation to deal with," added Kebaier. “The referee also blew with five minutes left in the first half and then he blew after 89 minutes, denying us practically seven or eight minutes of added time.
"His decision is inexplicable. I can't understand how he made his decision and we will see what happens now."