Tunisia had a chance to equalize but captain Wahbi Khazri missed a penalty.
Football enthusiasts were, however, shocked as Zambian referee Janny Sikazwe blew the end of the match at 89 minutes, one minute after he gave a Malian player a controversial red card.
The decision of the referee to end the game before additional time resulted in a confrontation with the Tunisian team.
Tunisian coach Mondher Kebaier was joined by his backroom staff in protesting the early end of the game grabbing the referee by the arm.
The referee had to be escorted off the pitch with security as chaos ensued after the game.
The decision of the match official has brought negative reactions about the AFCON on social media.
See reactions to the game below
The Confederation of African Football (CAF) reportedly instructed both Mali and Tunisia to return to the pitch to complete the entire duration of the game.
Mali returned but Tunisia chose not to. A decision is now expected from the African football governing body on the outcome of the game.