Balotelli had been left out of the Italy set-up by new coach Antonio Conte following the 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 debutants as Conte looks to freshen his squad ahead of the 2016 European Championships.
Italy sit second in Group H, but only on goal difference, behind Croatia after winning their three opening games.
Southampton striker Graziano Pelle scored Italy's winner on his debut away to Malta in their last outing as former Juventus handler Conte left Balotelli on the sidelines.
Croatia are considered Italy's toughest rivals in Group H and Conte said he expected Sunday's game to provide "answers" about his side's potential.
"It is important that this match gives us answers, and it is important that it takes place at this moment: we are putting ourselves back together after a disappointment [of the World Cup]," Conte said earlier this week.
"Croatia are doing well at the moment and they are a great team with a great outlook.
"Currently, we are behind other national teams like Germany, Spain, the Netherlands, Belgium and France. We are aware of the serious problems that Italian football has, but we know we have time to solve these problems.
"Now the important thing is that we qualify for the European Championships and then we will work on doing something extraordinary in the month we spend in France."
Goalkeepers: Gianluigi Buffon (Juventus), Mattia Perin (Genoa), Salvatore Sirigu (Paris Saint Germain/FRA)
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/FRA)
Strikers: Mario Balotelli (Liverpool/ENG), Sebastian Giovinco (Juventus), Ciro Immobile (Borussia Dortmund/GER), Graziano Pelle (Southampton/ENG), Simone Zaza (Sassuolo)