At 85 minutes of play, Sikazwe from Zambia ended the match only to recall the teams to the field to play the remaining minutes.
After he issued a red card to a Mali player, El Bilal Toure, Sikazwe blew the final whistle again ignoring his clock as it was not yet 90 minutes and didn't factor in the need for extra time.
Tunisian coach Mondher Kebaier and his technical staff rushed onto the field to confront Sikazwe.
In consultations with other officials, he recalled the teams to the pitch but Tunisia did not return to the field thus giving Mali a 1-0 victory.
In the encounter, Mali converted their spot-kick through Ibrahim Kone but the Carthage Eagles missed the chance to equalise through a 77th-minute penalty taken by Wahbi Khazri and saved by Mali's goalie Ibrahima Mounkoro.
In other matches, Ivory Coast beat Equatorial Guinea 1-0 and earlier Gambia silenced Mauritania with the same margin.
Coming up today, hosts Cameroon take on Ethiopia at 6 pm while Burkina Faso will battle it out with Cape Verde at 9 pm.