The tournament's organizing committee met late Thursday in Cameroon to ratify Mali's 1-0 win the previous day in its second Group F match after Zambian referee Janny Sikazwe's errors sparked confusion and anger.
While the game restarted after Sikazwe prematurely ended it after 85 minutes, he then blew full time for good when the game reached 89 minutes and 47 seconds. About three minutes of injury time had been expected.
The Tunisian players and coaching staff were incensed as the game ended early.
About 30 minutes later there was an attempt by officials to complete the outstanding minutes in Limbe, Cameroon on Wednesday.
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But Tunisia refused to come back out to restart the match, with the coach saying his players were already in their ice baths by then.
Tunisia lodged an official protest over Sikazwe's actions with CAF.
"After examining the protest of Tunisia and all the match officials report," the Confederation of African Football said in a statement, "the organizing committee decided ... to dismiss the protest lodged by the Tunisian team. To homologate the match result as 1-0 in favor of Mali."