To follow Brazil into the second round Australia will now be looking for a win against Croatia who drew nil-all with Japan in the earlier game.
Brazilian striker Adriano scored four minutes after halftime, while Fred sealed the match in the 89th minute.
The Socceroos didn't make it easy for the Brazilians, putting the world's best team under heavy second half pressure chasing an equaliser.
Substitute Harry Kewell perhaps had the best chance in the 57th minute, striking high but wide with the goal open after Brazilian goalkeeper Dida fumbled a high ball.
Kewell also went agonisingly close in the 68th minute, whipping a long-range attempt just over the bar.
Midfielder Marco Bresciano forced Dida into a sensational save with 12 minutes left, launching a spectacular scissors kick at goal only for the keeper to pull it out of the net with a diving save to his right.
Mark Viduka sent a glancing header from a Bresciano free-kick just wide inside the last ten minutes, then lofted another chance just over the bar.
Brazil made the game safe with a second goal when Fred tapped in after a shot that rebounded off the post. Brazil now tops Group F with two wins from two matches.
he Socceroos can advance to the second stage with only a draw in their final group match against Croatia in Stuttgart on Thursday (Friday AEST) if Japan cannot beat Brazil by two clear goals in its last game.
Croatia could only manage a 0-0 draw with Japan in Nuremberg earlier, meaning they must beat Australia to have any chance of advancing from the group.
The Socceroos lost defender Tony Popovic with injury five minutes before halftime, forcing a major change to the backline after coach Guus Hiddink started the match with five defenders.
Hiddink relegated Kewell, Bresciano and Luke Wilkshire to the bench for the match in three changes to the starting line-up which beat Japan 3-1 last week.