A laboured performance from Australia's midweek side put head coach Robbie Deans under increased pressure as Munster triumphed 15-6 at a wet and windy Thomond Park.
Former Australia Sevens captain Paul Warwick landed three penalties and two drop goals to down his countrymen and add another famous win to Munster's proud history.
With Australia smarting from their disappointing 35-18 defeat to England, Deans called on his second string to produce a winning performance ahead of their Test against Italy on Saturday.
But in heavy rain showers and a howling wind, the Wallabies looked disinterested at times, particularly during a second half which a largely youthful Munster outfit comfortably dominated.
The hosts lacked the necessary invention to breach the Australian try-line, going closest through a series of pick-and-go efforts close to the posts. In the end, Warwick's kicking haul was enough to seal Munster's fourth victory over Australia, after previous wins in 1967, 1981 and 1992.