Senegal were ruled to have forfeited the game in Rabat on January 18th because they walked off the pitch in protest at a potentially decisive penalty awarded to opponents Morocco.
They returned after 14 minutes to win the match 1-0, but the appeal board of African soccer's governing body (CAF) last week replaced that result with a 3-0 victory for Morocco.
"The FSF appeal seeks to set aside the CAF decision and declare the FSF winners of AFCON. It also requests an immediate suspension of the time limit to submit an appeal brief until the CAF decision is notified with full grounds," the CAS said in a statement.
"A CAS Arbitral Panel will be appointed to consider this matter. Following this, a procedural calendar will be established."
The Senegalese government earlier called for an inquiry into the removal of the title.
The FSF's lawyers will address a press conference in Paris on Thursday.