The Netherlands midfielder, who has one substitute appearance to his name so far, will line up alongside Massimo Ambrosini and Urby Emanuelson in the hosts’ midfield, while Ignazio Abate replaces Mattia De Sciglio in defence.
Stephan El Shaarawy has also been chosen to start alongside Giampaolo Pazzini in attack ahead of Bojan Krkic will have to wait for his first start in Milan colors after being named on the bench by Massimiliano Allegri.
Andrea Consigli begins the match in goal for Atalanta, marking his 200th appearance for the club, who have only picked up a single point from their two Serie A fixtures so far.
Milan (4-3-1-2): Abbiati; Abate, Bonera, Acerbi, Antonini; De Jong, Ambrosini, Emanuelson; Boateng; El Shaarawy, Pazzini.
Subs: Amelia, Niang, Yepes, Mexes, Zapata, Mesbah, De Sciglio, Flamini, Nocerino, Constant, Valoti, Bojan
Atalanta (4-4-1-1): Consigli; Bellini, Lucchini; Manfredini, Brivio; Raimondi, Cigarni, Biondini, Bonaventura; Moralez; Denis.
Subs: Frezzolini, Polito, Stendardo, Matheu, Ferri, Cazzola, Scozzarella, Troisi, Parra, De Luca