The Pumas were leading 31-7 at halftime after scoring four tries and a penalty but were overrun in the second half and could only manage a penalty to counter Australia's five tries.
The Pumas, who needed just a draw to guarantee the Australians finished in last place, ended up losing 45-34 in what was the biggest comeback in Rugby Championship history.
"We played the way we wanted and the way we trained during the week," Pumas lock Guido Petti said of their first half performance. "But in the second half it was the opposite."
Despite the second half in Salta, the Argentines still performed better than expected this year, thanks in large part to new coach Mario Ledesma, who led his side to wins at home to South Africa and away to Australia.
Their inability throughout the championship to close down games from strong positions, however, was obvious and recurring and speaks to a lack of depth and perhaps also of fitness or focus.
Saturday's loss could also either make or break a team who have been drawn in arguably the toughest pool at next year's World Cup where they face England, France, the United States and Tonga and flanker Pablo Matera said his team would have to use it as a lesson.
"We started off very well, we knew that if we did things right then we could hurt them," said Matera.
"At the end of the first half they started to play the ball from side to side, we lost focus and we couldn't get back into the game."
"The only thing I wanted was for the team to play well again, end the Rugby Championship playing our own game, but when they started scoring tries our side lost focus and we had to chase them. Its very hard to take.
"We didn't end this as we wanted. We have to use this loss to get better."
(Reporting by Ramiro Scandolo, writing by Andrew Downie; Editing by Greg Stutchbury)
