The Aussie played the first 45 minutes of the Socceroos 2-0 defeat against Tunisia, to finish pointless and bottom of their group.
Earlier Viduka had suggested that he would put his country before his club in a bid to reach the World Cup finals in Germany next year.
"There are a lot of us who have got to the point were we are realising this is our last shot at the World Cup finals.
"We are prepared to do anything to get there. Making the World Cup with Australia is my biggest goal at the moment and I will not let anything stand in my way."
The Socceroos play two play-off games against the Solomon Islands in September with potenially a further two to follow in November, so Viduka would be unavailable for a minimum of two weeks in the first half of the season.
Mark Schwarzer, who could also take part in the play-off games, was rested for last nights game and did not add to his record for the number of caps gained by a Boro player. The record now stands at 28.