Onana, on loan at Trabzonspor from Manchester United, is one of several experienced players dropped for the December 21 to January 18 tournament, including striker Vincent Aboubakar, who has been a mainstay of the team for the last 15 years.
The changes come after Cameroon failed to qualify for the 2026 World Cup in the United States, Mexico and Canada.
Manchester United winger Bryan Mbeumo is in the squad along with Brighton midfielder Carlos Baleba.
The country's football federation President Samuel Eto’o has made no secret of his desire to replace Brys, 63, since the latter's April 2024 appointment by the sports ministry and has tried several times before.
Emboldened by his re-election as president last weekend, Eto’o has had another go and replaced the Belgian with 56-year-old Pagou, who has managed in Cameroon's domestic league and will be assisted by Martin Ntoungou Mpile.
Cameroon open their Group F campaign at the Cup of Nations finals against Gabon in Agadir on December 24. They also have defending champions Ivory Coast and Mozambique in their pool.
Cameroon squad:
Goalkeepers: Devis Epassy (Dinamo Bucharest), Simon Omossola (St Eloi Lupopo), Simon Ngapandouetnbu (Montpellier), Edouard Sombang (Colombe Du Dja)
Defenders: Samuel Kotto (Gent), Gerzino Nyamsi (Lokomotiv Moscow), Jean-Charles Castelletto (Al-Duhail), Nouhou Tolo (Seattle Sounders), Flavien Enzo Boyomo (Osasuna), Mahamadou Nagida (Rennes), Christopher Wooh (Spartak Moscow), Junior Tchamadeu (Stoke City), Darlin Yongwa (FC Lorient)
Midfielders: Martin Ndzie (Rapid Vienna), Carlos Baleba (Brighton), Arthur Avom (FC Lorient), Eric-Junior Dina Ebimbe (Brest), Brice Ambina (Valerenga), Jean Junior Onana (Genoa), Olivier Kemen (Istanbul B.B)
Forwards: Bryan Mbeumo (Manchester United), Christian Bassogog (Al-Okhdood), George-Kevin N’koudou (Al-Diriyah), Danny Namaso (Auxerre), Frank Magri (Toulouse), Karl Etta Eyong (Levante), Christian Kofane (Bayer Leverkusen), Patrick Soko (Almeria)