Brett Emerton grabbed a brace while Harry Kewell also found the back of the net before Khalfan Ibrahim claimed a late consolation for the hosts.
The Socceroos are now three points clear of both Qatar and Iraq.
But with the top two advancing to the next qualifying stage and Qatar and Iraq to play each other next week, Australia will go through regardless of their final match against China next Sunday in Sydney.
The Blackburn winger scored once in each half to bury the Qataris, while Kewell added the third on 74 minutes to put Pim Verbeek's side a step closer to the 2010 World Cup finals in South Africa.
Qatar scored a late consolation goal through Khalfan Ibrahim in the 89th minute.