Dragons boss Gary Speed was able to pick an almost full-strength side with the likes of Gareth Bale, making a first appearance in 10 months, Craig Bellamy and captain Aaron Ramsey all starting.
But the hosts struggled to break down a well-organised Socceroos defence as they fell to a side 89 places above them in the world rankings.
Tim Cahill volleyed the opener for Holger Osieck's side just before half-time, with Wales mystified by a penalty appeal for a foul on Bale being waved away seconds earlier, before substitute Robbie Kruse tapped in the second just after the hour mark.
Darcy Blake pulled a goal back for the hosts as they finished strongly, but it was not enough to prevent a fourth defeat in five games for boss Speed.
The game had a low-key feel to it in the early going and the first incident of note was a clumsy tackle on Scott McDonald by David Vaughan after 15 minutes, for which the Sunderland midfielder was lucky not to be booked.
The first shot on goal came in the 19th minute but Luke Wilkshire's free-kick hit the wall before Carl Valeri dragged the first genuine chance wide.
Wales eventually had an effort on goal as Bellamy cut inside from the right, but his shot was blocked by Matthew Spiranovic.
There was finally something for the sparse crowd to get excited about as Wilkshire produced a thunderous dive from the right side of the area which cannoned to safety off the post with Wayne Hennessey beaten.
But Wales felt they should have been awarded a penalty just before the break when Bale went down under a challenge from Emerton, but Estonian official Kristo Tihver waved away the appeals.
And to the home side's chagrin the Socceroos went straight up the other end to grab the opener as Cahill volleyed home his 24th international goal from close range as he latched on to a Wilkshire cross.
Ramsey was withdrawn at the break with Jack Collison coming on, while Australia introduced former Wales Under-21 cap Rhys Williams, who was roundly booed by the home crowd.
The visitors should have doubled their lead just two minutes after the restart as a defensive lapse forced Hennessey to deny Kruse before the post kept out Valeri.
Collison lofted over after some good work down the right before a surging Bale run was halted by a cynical Michael Zullo challenge that earned the full-back a booking.
But the visitors were providing the greater attacking threat and they deservedly grabbed their second goal after 61 minutes.
McDonald was given space on the right of the area and his cross was palmed straight into the path of Kruse by Hennessey, giving the forward a simple tap in.
Bellamy had an effort from a tight angle blocked by Spiranovic as Wales sought a response, after Bale, who was making more of an impact after a quiet first half, produced another threatening run.
Wales set up an exciting finish when substitute Blake headed home after a corner bobbled its way through to him in the 82nd minute, the Cardiff defender claiming a first international goal on his home ground.
Spiranovic headed just over his own bar from a Bale cross as Wales piled on the pressure but the visitors held out for the win in the first meeting between the sides.