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Cardiff - Wales coach Warren Gatland said his embattled side paid the price for naivety as they again went close but ultimately failed to take a southern hemisphere scalp and end a torrid few months on a high.
Time was almost up at the Millennium Stadium when Australia's Kurtley Beale took an inside pass from Dave Dennis and left a tired Welsh defence to score the game's only try and secure a 14-12 victory.
The defeat capped a miserable month for Wales, who celebrated the Six Nations Grand Slam in March but have suffered seven successive defeats since.
The heartbreaking loss also cost them a place in the world's top eight, meaning they now face a tough World Cup group when the draw for the 2015 tournament is made on Monday.
Gatland, absent from the first two Tests of the month while on British and Irish Lions duty, rued the defensive lapses which allowed Australia, pinned back deep in their own half with the clock ticking down, to progress up-field and set up the winning score.
Wales looked to have repelled the first onslaught when they regained possession, only for much-criticised flyhalf Rhys Priestland to miss touch with a clearance downfield. Back came the Wallabies with fullback Berrick Barnes making a half-break before feeding Mike Harris who set Dennis free to set up Beale.
"The disappointing thing for me is that we have turned over a lineout - and then it was obvious they were going to run the ball from their own goalline," Gatland told a news conference.
"It was a little bit of naivety. We have allowed them to relieve the pressure and gain 30 metres. We should have defended the frontline better. Even in the last couple of plays there were (Welsh) players hanging back. We needed 14 players on the frontline."
Wales lost three Tests to Australia in June, returning home empty-handed despite two close encounters - a 25-23 loss in Melbourne followed by a 20-19 defeat in Sydney.
Beaten but not bowed, Wales had high expectations of regaining momentum in November but things have gone from bad to worse since Argentina, fresh from rubbing shoulders with the southern hemisphere giants in the Rugby Championship for the first time, waltzed into Cardiff and sprung a 26-12 surprise.
A host of injuries, especially to key players in the pack - including Adam Jones and Dan Lydiate - robbed the Welsh of cohesion and their mistakes were then ruthlessly exploited by a physical Samoa side.
The Samoans left the Welsh bruised and battered in a 26-19 win and the alarm bells were well and truly ringing across the proud rugby nation.
A battling second-half effort in a loss to New Zealand last week gave Wales some hope they could find their lost fire and Gatland said the Welsh had not become a bad side, despite the run of defeats.
"Had we won today we would still have been disappointed, dropping a couple of games," he said.
"The second half last week and today we played some good rugby. We have shown we are a good side.
"But we need to be a lot smarter at the death - a few times it's happened against Australia when we haven't been able to finish it off - when we should have been more clinical."
