Tunisian Football Association president Wadie Jary has been banned from all activities relating to the Confederation of African Football.
It follows Caf's ultimatum for the Tunisian FA to apologise for accusing the body of cheating or be banned from the 2017 Africa Cup of Nations.
On Friday, Caf gave a deadline of 31 March for the Tunisian FA to apologise.
Tunisia made the allegations over a controversial penalty in a 2-1 quarter-final defeat by Equatorial Guinea.
The game's referee has been banned for six months for "poor performance".
After a meeting on Wednesday, the Tunisian FA refused to apologise with a spokesman saying the team had "suffered scandalous injustice from referees".
Caf, which fined Tunisia after players confronted referee Rajindraparsad Seechurn after the final whistle, had wanted the 2004 champions to apologise for "insinuations of bias and lack of ethics against Caf and its officials, or to present irrefutable evidence to substantiate the accusations".
African football's governing body said it had been sent two letters by the Tunisian FA after the match, with the second asking for an investigation and suggesting Caf and its officials "were questionable and biased against Tunisia in general".
Caf fined Tunisia $50,000 (£33,000) for what it termed "the aggressive attitude of some supporters in the stands, invasion of the pitch after the final whistle by players and substitutes of the Tunisian team - insulting the referee of the match and trying to physically assault him - and the regrettable behaviour of the president of the Tunisian Football Federation, Wadie Jary".
The Tunisian federation was also ordered to pay for damages after their players broke a changing-room door and a fridge.
The ugly scenes came after Mauritian referee Seechurn had awarded the penalty in stoppage time when Ali Maaloul was harshly ruled to have fouled Ivan Bolado when Tunisia were leading 1-0 and, after equalising from the spot through Javier Balboa, hosts Equatorial Guinea went on to win in extra time.
Qualifying for the 2017 tournament starts in June.