Balotelli has been left out of the Italy set-up by new coach Antonio Conte following their first round exit from the World Cup under former coach Cesare Prandelli.
Cerci failed to make the trip to Brazil but is included in a 26-man squad named on Sunday night by the Italian Football Federation (FIGC).
Torino defender Emiliano Moretti and midfield pair Andrea Bertolacci (Genoa) and Roberto Soriano (Sampdoria) are among the squad debutants as Conte looks to freshen his squad ahead of the 2016 European Championships.
Italy sit second on Group H, but only on goal difference, behind Croatia after winning their three opening games.
Italy squad for Croatia in Milan on November 16:
Goalkeepers: Gianluigi Buffon (Juventus), Mattia Perin (Genoa), Salvatore Sirigu (Paris Saint Germain)
Defenders: Giorgio Chiellini (Juventus), Emiliano Moretti (Torino), Angelo Ogbonna (Juventus), Andrea Ranocchia (Inter), Daniele Rugani (Empoli)
Midfield: Andrea Bertolacci (Genoa), Giacomo Bonaventura (Milan), Antonio Candreva (Lazio), Alessio Cerci (Atletico Madrid/ESP), Matteo Darmian (Torino), Daniele De Rossi (Roma), Mattia De Sciglio (Milan), Stephan El Shaarawy (Milan), Claudio Marchisio (Juventus), Marco Parolo (Lazio), Manuel Pasqual (Fiorentina), Roberto Soriano (Sampdoria), Marco Verratti (Paris Saint Germain)
Strikers: Mario Balotelli (Liverpool), Sebastian Giovinco (Juventus), Ciro Immobile (Borussia Dortmund), Graziano Pelle (Southampton), Simone Zaza (Sassuolo)
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