Morocco were declared African champions on Tuesday after the Confederation of African Football's Appeal Board upheld their protest and found Senegal's walk-off during the final on January 18 were grounds for them to be disqualified.
The match result was declared 3-0 in favour of the hosts.
Senegal won the final in Rabat with an extra-time goal, but not before staging a 14-minute walk-off after a penalty was awarded against them in stoppage time at the end of the regulation 90 minutes.
The protest was instigated by coach Papa Bouna Thiaw, who was subsequently handed a lengthy ban, and led to Senegal's veteran striker Sadio Mane emerging as a hero as he attempted to get his teammates back onto the field.
Once Senegal returned to the pitch, the referee allowed play to continue with Morocco squandering the last-gasp penalty and the encounter then going to extra time, with midfielder Pape Gueye netting the 94th-minute winner.
However, CAF's Appeal Board said by walking off, Senegal contravened tournament regulations and forfeited the game.
"The Senegalese Football Federation denounces this unfair, unprecedented, and unacceptable decision, which casts a shadow over African football," it said in a statement on Wednesday.
"To defend its rights and the interests of Senegalese football, the federation will initiate an appeal as soon as possible before the Court of Arbitration for Sport in Lausanne."
The Swiss-based CAS had to intervene in 2019 when Moroccan club Wydad Casablanca walked off in the second leg of the African Champions League final, also protesting against VAR.
In that case, they refused to play on, and the referee declared opponents Esperance as winners, but CAF's executive committee then surprisingly ordered a replay.
Esperance took the matter to CAS and were declared champions, with CAF embarrassingly rebuked for attempting to override the referee's decision.
The decision by Congolese referee Jean-Jacques Ndala to continue with the Cup of Nations final in January, rather than stop it and declare Morocco winners after Senegal's walk-off, will likely feature strongly in any arguments for a reinstatement of Senegal as champions.
The Laws of the Game state the referee's decision is final.
"No one could have imagined such a statement two months after the final," said veteran coach Claude Le Roy, who managed Senegal between 1988 and 1992.
"For years, all the refereeing decisions have been flouted by the CAF," he said on French television.
