Senegalese Football Federation spokesman Mbacke Seck linked Fadigaâ€™s exclusion to his failure to secure a regular top-level spot with the English club.
Portsmouth midfielder Salif Diao and Pape Malick Diop of French second division side Lorient were both omitted due to injury.
Senegal are in Group D with Nigeria, Ghana and Zimbabwe at the finals which start in Egypt on Jan. 20.
In October, the Senegalese failed to qualify for the World Cup finals in Germany beginning in June.
Meanwhile, Barcelona striker Samuel Etoâ€™o will stand down from club commitments in order to play for Cameroon at next monthâ€™s African Nations Cup, state radio quoted him as saying.
The 24-year-old has been in prolific form for his club, scoring 17 goals in as many games to help the champions top the Primera Liga table, and is shortlisted for what would be a record-breaking third African Footballer of the Year award.
â€œIt has never been a question for me not to go to Egypt (for the African Nations Cup),â€ Cameroonian state radio reported Etoâ€™o as telling journalists in Garoua during a Christmas trip to his home country.
Fadiga dropped, Etoâ€™o to play