Jozo Šimunović, who moved this summer from Croatian champions Dinamo Zagreb to Scottish champions Celtic, originally replaced the injured Liverpool's defender Dejan Lovren in Ante Čačić's squad for matches with Bulgaria and Malta.
However, Šimunović will also miss out due to ankle injury, and new Croatia head coach Čačić decided to add Duje Ćaleta-Car of Red Bull Salzburg to the senior national team, from Nenad Gračan's U-21 squad.
Croatia plays at home against Bulgaria on 10 October and away to Malta on 13 October.
Luka Capan of Lokomotiva Zagreb was subsequently added to Croatia U-21 squad, and Gračan eventually also called up Rijeka defender Frane Ikić. Injured striker Marko Kolar was replaced by Lokomotiva's Ivan Fiolić. Croatia U-21 awaits qualifier against San Marino and friendly against Russia.