The Boro frontman takes over from Craig Moore who has just battled back from injury. Manager Gus Hiddink felt it was more important for Moore to regain his place in the squad before he took the captains armband back.
Viduka did captain the Socceroos on a number of occasions during the qualifying campaign.
Mark Schwarzer is also a member of the Socceroos squad heading for Germany, while ex-Boro midfielder Luke Wilkshire, now with Bristol City, has also won a place in the squad.