Ahli claimed a 2-1 victory over Esperance in the first leg of the Champions League semi final but the match was marred by some unfortunate incidents in the visitors' stands.
TV cameras caught a dozen of Esperance supporters beating up two stewards after Ahmed Fathi gave Ahli a 2-0 lead before the Tunisians narrowed the gap through a goal from captain Oussama Darragi.
They also ripped up seats and threw them onto the pitch before letting off illegal flares.
"On behalf of the Tunisian federation, I apologize for what happened from the Esperance supporters during the Ahli game," FTF chairman Ali Hafsi told Nile Sports.
"The people who caused the riots do not belong to sports. We will hold an investigation into those incidents to prevent them from happening again."
Tunisian ambassador to Egypt Mongi Bedoui also deplored the actions of a 'minority of Esperance fans'.
"They were treated very well after their arrival in Egypt but their reply was wholly unacceptable," he said.
"I want to thank the Egyptian security personnel for the way they handled the matter."
The two stewards are believed to be receiving treatment in hospital but their injuries are not serious, according to media reports.
Eleven Esperance fans were detained by Egyptian police and face charges of assaulting security personnel and causing unrest.
The games between Egyptian teams and their counterparts in North Africa are usually tense due to a heated football rivalry.
However, the Egyptian-Tunisian contests barely witness chaotic scenes.
Ahli famously defeated Esperance on the away goal rule after a 1-1 aggregate draw in the 2001 Champions League semis before going on to lift the trophy.
Both sides also met twice in the group stage of Africa's premier club competition in 2007.
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