Coach Robbie Deans paid the price for fielding a weakened team which saw Quade Cooper, David Pocock and James Horwill left out entirely and Will Genia and Kurtly Beale only included among the replacements.
Samoa led from the third minute at the ANZ Stadium, with Leicester's Alesana Tuilagi and Sale's Paul Williams scoring first-half tries.
Digby Ioane scored just before the break for the hosts but Samoa added a further brace of tries in the first 15 minutes after the interval through lock Kane Thompson and centre George Pisi.
The Wallabies only managed one more try with 10 minutes remaining when Matt Giteau crossed the Samoan line. Giteau finished with a personal tally of 18 points courtesy of that try, two conversions and three penalties after he started at fly-half instead of Cooper but 13 of Australia's 23 points came when Samoan second row Dan Leo had been sin binned.
The result was in stark contrast to the scoreline when the two teams met at the same venue last year, with the Wallabies hammering Samoa 74-7 on that occasion.
Australia host South Africa in the opening leg of the Tri Nations this coming Saturday and Sunday's clash had been viewed as the perfect warm up to the series with the Springboks and the All Blacks.
The Wallabies were expected to be able to get rid of any cobwebs from not having played together in 2011 but to also run out comfortable winners at the same time. The fact that neither the performance nor result came anywhere meeting national expectations will heap added pressure on Deans and ensure the build up to the World Cup will now be a less comfortable one as far as media and public pressure are concerned.
Australian Rugby Union chief executive John O'Neill said last week that a deal to keep Deans as Wallaby coach until after the 2013 Lions tour had been agreed in principle, but critics such as legendary wing David Campese had publicly called for Ewen Mckenzie to take over after he led the Reds to Super 15 glory and Sunday's result will add prominence to those opinions.