Adriano notched his first goal of the tournament four minutes into the second half after the South Americans had endured a frustrating first-half against Guus Hiddink's [ Images ] men.
Substitute Fred wrapped up the win in the 89th minute, rolling home a rebound after a Robinho [ Images ] shot came back off a post.
Striker Ronaldo [ Images ] played poorly and was substituted for the second game running in another generally unconvincing performance by Brazil, who beat Croatia [ Images ] 1-0 in their opening game.
Australia, who face Croatia in their last game, have three points while Japan [ Images ] and Croatia have one each in Group F.
Brazil's best first-half move came in the third minute.
Ronaldo controlled the ball on his chest and flicked the backwards to Kaka [ Images ] who volleyed wide from the edge of the penalty area.
If the ball had gone in, the game could have taken a completely different course.
Instead, Australia packed the midfield and hustled Brazil out of their stride with tenacious marking and tackling.
Brazilian pair Ronaldo and Ronaldinho [ Images ] were both subdued with only Kaka's penetrating runs offering any threat.
Ronaldo, who had a dismal match against Croatia, was again out of sorts and at one point had a heated argument with coach Carlos Alberto Parreira on the touchline.
His frustration was complete with a yellow card for playing on after he had been flagged offside.
The second half was only four minutes old when Brazil got the breakthrough they badly needed.
Ronaldinho picked out Ronaldo, who held off his marker and rolled the ball across the face of the penalty area to Adriano.
The Inter Milan [ Images ] striker, also struggling until then, took one touch and placed a low shot beyond goalkeeper Mark Schwarzer's left hand.