Glasgow's Graeme Morrison, Scott Lawson and Rory Lamont went over for tries but it wasn't enough to stop the Australians gaining a confidence boost before Saturday's Test match at Murrayfield.
Both sides had entered the fray after preparations which were less than ideal.
Scotland coach Henry Edwards was forced to contend with losing skipper Rory Lawson and flanker Ally Strokosch to the senior set-up and the makeshift nature of their line-up showed.
The Wallabies were back in action just two days after their bruising defeat at the hands of Ireland at Lansdowne Road, but the Scots were unable to stretch them.
Scotland were handed an instant three-point gift thanks to a simple penalty by stand-off Gordon Ross when the visitors sneaked offside at a maul.
But the Australians hit back to snatch the initiative with two penalties in quick succession from Cameron Shepherd.
First, the Scots were pressured into making three mistakes during a frantic passage of play.
And when referee Andrew Small spotted hands being used in a ruck, Shepherd was left with a formality of a kick.
He repeated the feat after the tourists had strung together a series of well-drilled phases in enemy territory.
Suddenly, the Wallaby second-stringers clicked into gear and they effectively snuffed out the Scottish challenge with two tries before the interval.
Following several close calls, it was prop Rod Blake who claimed the opening touchdown from close range in the wake of some excellent off-loading skills.
Then three minutes from the break, poor work from full-back Calum MacRae set up their next score.
MacRae was snared in possession as he tried to take on two rivals on his own, and after the ensuing scrum Mat Rogers created the time and space for Morgan Turinui to send winger Drew Mitchell cruising over the line.
Australia made a storming start to the second half, taking less than a minute to stretch their lead.
The home markers were absent as Mitchell jigged past at least four of them on his way to the target. Shepherd converted.
Scotland refused to buckle completely and they replied in positive fashion with a solo effort from centre Graeme Morrison.
But soon the visitors were back in potent form to add to more scores. Blake was driven over to record his double - Shepherd added the goal, then proved his all-round talent by taking advantage of more hesitant defending.
As play became disjointed, hooker Scott Lawson clawed back five more points for the Scots at the end of a pushover move.
The end-to-end action continued as scrum-half Brett Sheehan dashed under the crossbar for the visitors' sixth try, again converted by Shepherd.
But the home fans were on their feet as they watched Rory Lamont claim the best try of the contest for Scotland, with Ross slotting the kick.