The ruling was made this week by Caf after January's controversial final, where Senegal won in extra-time after leaving the pitch for 15 minutes following a penalty awarded in the last minutes of normal time to Morocco. Brahim Diaz, after Senegal returned to the pitch, had his spotkick saved which sent the final into extra-time.
In a statement the Senegalese government said the "unprecedented and exceptionally serious decision" was based on "a manifestly erroneous interpretation of the regulations, leading to a grossly illegal and deeply unjust decision".
It said: "Senegal unequivocally rejects this unjustified attempt at dispossession."
Meanwhile, in a statement on Wednesday, FRMF (the Moroccan Federation) said it "welcomes" the ruling by Caf, which "upholds respect for rules that are necessary for the proper functioning of international competition."
It added: "This decision helps to clarify the framework applicable to similar situations in the future and contributes to the consistency and credibility of international competitions, particularly African football."
"By calling into question a result achieved at the end of a match that was properly played and won in accordance with the rules of the game, the Caf seriously undermines its own credibility," Senegal government spokeswoman Marie Rose Khady Fatou Faye said in a statement.
"Senegal unequivocally rejects this unjustified attempt at dispossession," she said, while calling for "an independent international investigation into suspected corruption within the CAF's governing bodies".
In her statement, Faye called the matter "a grossly illegal and profoundly unjust decision".
"Senegal will pursue all appropriate legal avenues, including before the competent international courts, to ensure that justice is served and that the primacy of sporting results is restored", she said.