Scotland scored in the first minute with a penalty from Gordon Ross, but Australia quickly took the lead, notching up two penalties and tries from Rodney Blake and Drew Mitchell after good work by captain Morgan Turinui, one of the players in the World XV squad for their match against South Africa at Leicester City's Walkers Stadium on December 3.
Australia, who included experienced internationals Mat Rogers and David Lyons in the starting XV and had Clyde Rathbone, Al Baxter and Phil Waugh on the bench, led 18-3 at half-time and quickly added to the advantage when Mitchell grabbed his second try of the night.
Centre Graeme Morrison then crossed for a Scottish try before quick Aussie scores from man of the match Blake and Cameron Shepherd.
Scott Lawson and Rory Lamont popped up with the hosts' other tries on the night, either side of a try from Australia scrum-half Brett Sheehan.
Scotland A: Calum MacRae (Border Reivers); Nikki Walker (Ospreys), Graeme Morrison, Rory Lamont, Thom Evans (all Glasgow Warriors); Gordon Ross (Castres), Sam Pinder (Glasgow Warriors); Alasdair Dickinson (Edinburgh Rugby), Scott Lawson (Glasgow Warriors), Craig Smith (Edinburgh Rugby), Craig Hamilton (Border Reivers), James Hamilton (Leicester Tigers), Andrew Wilson (Glasgow Warriors), Scott Gray (Border Reivers), Jon Petrie (Glasgow Warriors, captain).
Reps: John Barclay (Glasgow Warriors) for Gray 47min, Graeme Beveridge (Glasgow Warriors) for Pinder 47min, Ed Kalman (Border Reivers) for Smith 60min, Andrew Hall (Newport-Gwent Dragons) for Wilson 61min, Colin Gregor (Glasgow Warriors) for Evans 69min, Garry Law (Border Reivers) for MacRae 79min.
Australia A: Cameron Shepherd; Adam Ashley-Cooper, Morgan Turinui (captain), Gene Fairbanks, Drew Mitchell; Mat Rogers, Brett Sheehan; Nic Henderson, Tatafu Polota-Nau, Rodney Blake, James Horwill, Mitchell Chapman, Scott Fava, Stephen Hoiles, David Lyons.
Reps: Mark Chisholm for Lyons 31min, Clyde Rathbone for Rodgers 61min, Josh Valentine for Sheehan 66min, Tai McIsaac for Blake 71min, Al Baxter for Chisolm 71min. Unused: Phil Waugh, Mark Gerrard