Zukanovic was unable to travel with his national squad to their training camp in the United States after being refused a visa.
The Gent defender was quoted as blaming the situation on the Bosnian football federation, who subsequently responded with a statement that confirmed the player would no longer be needed in Brazil.
Bosnia coach Safet Susic had originally named 24 players in his provisional squad, so the absence of Zukanovic means the other players who were originally selected have been retained.
Susic's men reached the finals after topping their UEFA qualifying group ahead of Greece, who subsequently made it to Brazil via the play-offs.
Bosnia face Mexico in their final warm-up match on Wednesday, before taking on Argentina, Nigeria and Iran in Group F at the World Cup.
Squad in full:
Goalkeepers: Asmir Avdukic (Borac Banja Luka), Asmir Begovic (Stoke City), Jasmin Fezjic (Aalen).
Defenders: Muhamed Besic (Ferencvaros), Ermin Bicakcic (Eintracht Braunschweig), Sead Kolasinac (Schalke), Emir Spahic (Bayer Leverkusen), Toni Sunjic (Zorya), Ognjen Vranjes (Elazigspor).
Midifelders: Anel Hadzic (Sturm Graz), Izet Hajrovic (Galatasaray), Senijad Ibricic (Erciyespor), Senad Lulic (Lazio), Haris Medunjanin (Gaziantepspor), Zvjezdan Misimovic (Guizhou Renhe), Mensur Mujdza (Freiburg), Miralem Pjanic (Roma), Sejad Salihovic (Hoffenheim), Tino Susic (Hajduk Split), Edin Visca (Istanbul BB), Avdija Vrsajevic (Hajduk Split).
Forwards: Edin Dzeko (Manchester City), Vedad Ibisevic (Stuttgart).
