As a result, Malaga defender Eliseu and PAOK Salonika midfielder Vieirinha were called up by coach Paulo Bento to join Portugal's squad.
Zenit St Petersburg's Danny had a knee injury while Silvio was considered "unfit for competition", according to a Portuguese football federation statement.
"I was checked and will be leaving the training camp now due to a groin pain. I do so with regret; no player likes to miss out on such decisive matches as these two but I think we will manage to qualify," Silvio told journalists.
Portugal play the first match in Zenica on Friday and host the Bosnians four days later in Lisbon.
Goalkeepers: Eduardo (Benfica), Beto (Cluj), Rui Patricio (Sporting).
Defenders: Bruno Alves (Zenit St. Petersburg), Joao Pereira (Sporting), Fabio Coentrao (Real Madrid), Rolando (Porto), Eliseu (Malaga), Pepe (Real Madrid), Sereno (Cologne).
Midfielders: Carlos Martins (Granada), Joao Moutinho (Porto), Miguel Veloso (Genoa), Raul Meireles (Chelsea), Ruben Micael (Real Zaragoza), Ruben Amorim (Benfica), Vieirinha (PAOK Salonika)
Forwards: Cristiano Ronaldo (Real Madrid), Helder Postiga (Real Zaragoza), Nani (Manchester United), Ricardo Quaresma(Besiktas), Nuno Gomes (Braga), Hugo Almeida (Besiktas).