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).