Australia's backline was simply superb, man-of-the-match second five-eighths Matt Giteau scoring two tries, while hooker Jeremy Paul, prop Greg Holmes, fullback Chris Latham and lock Mark Chisholm also crossed.
Centre Stirling Mortlock also added 16 points with the boot to help the Wallabies keep their Tri-Nations' hopes alive after their disappointing 12-32 first-up loss to the All Blacks.
The forecast showers came just before kickoff and made conditions difficult for the players, both sides making several handling errors in the opening stages.
First five-eighths Stephen Larkham opened the scoring after eight minutes with a 40-metre dropped goal, before the kicking wobbles continued for Mortlock.
The Australian vice-captain worked on his kicking during the week, but it didn't show on his first attempt, slamming it straight into the upright.
Latham's boot, meanwhile, was red hot, putting a massive 60m punt into touch and giving the Wallabies a line-out five metres from the South African line.
Paul then crossed for the opening try of the night on the back of a rolling maul, and Mortlock finally found his range to give Australia a 10-0 lead.
Another superb Wallabies kick set up the next score, fullback Percy Montgomery coughing up a cross-field kick just metres from the Australian line.
Moments later Australia received a penalty, which Mortlock converted.
Some superb Wallabies half work then led to a try for Holmes, with Larkham stepping the Springbok defence and offloading to his captain, and halfback, George Gregan, who sent the forward over.
The Springboks were reduced to 14 men on the half-hour when Victor Matfield was sinbinned for a deliberate knock-on, and Giteau wasted little time making them pay, dancing around the defence to score his first.
Trailing 30-0 at half-time, the Springboks came out full of flair in the second half, dominating the first 10 minutes but blowing several scoring opportunities.
The best chance came when the visitors had a scrum just five metres from the Wallabies' line, but Australia pinched the ball and relieved the pressure.
Centre Jaque Fourie also looked like scoring when he broke clear through the middle, but some wayward passes again ensured they were kept scoreless.
With the South African attack subdued, Australia counter punched, and they were would have gone further ahead if not for the heroic efforts of replacement Fourie Du Preez, who held up both replacement halfback Sam Cordingley and lock Nathan Sharpe in-goal.
Finally, however, Australia crossed again, Latham dotting down, and the floodgates opened, Giteau crossing for his second before Chisholm completed the rout.
Australia 49 (Matt Giteau 2, Jeremy Paul Greg Holmes, Chris Latham, Mark Chisholm tries; Stirling Mortlock 5 con, 2 pen; Stephen Larkham dropped goal) South Africa 0.