Australia crept into the semi-finals with late penalty to send South Africa out
South Africa 9 Australia 11
And O'Connor stepped up and nervelessly sent his kick between the uprights as the Wallabies made it six victories in seven matches against their Tri-Nations rivals.
It was hardly a great advert for the Tri-Nations as the World Cup's second and third favourites produced a messy and chaotic spectacle that failed to live up to expectation.
The Wallabies prevailed despite a dismal performance from fly-half Quade Cooper, who was off-key in just about every department of his game.
South Africa fielded the most capped starting line-up in Test history, consisting of 836 appearances, but even that vast experience was not enough against determined Australia.
The Springboks' power game was on display as they pounded away at Australia's defence in the opening 10 minutes.
South Africa were in control until Burger spilt the ball close to his own line following a line-out.
As quick as a flash Australia pounced, Pat McCabe taking a pass from Radike Samo and driving forward before slipping to Horwill who crashed over.
O'Connor missed the conversion but landed a penalty soon after to nudge Australia 8-0 ahead.
Panic broke out in the Springboks' ranks once more when Kurtley Beale glided into space and had it been a back in support rather than hooker Stephen Moore they would have been in for a second.
Only a last-gasp intervention from David Pocock prevented Burger from scrambling over after Spies had broken from the back of a scrum.
A lengthy spell of kicking ended when O'Connor and Will Genia slipped through a clutch of green shirts, only for Cooper to knock on as he sought to link up with his half-back partner.
South Africa made hard work of capitalising on space down the left, preventing Bryan Habana from making the most of a promising moment.
Habana was smashed by Samo and in the 36th minute the Springboks were finally off the mark when Steyn landed a penalty.
The Tri-Nations rivals threw everything at each other as the second half began in brutal fashion.
South African celebrations at a try for Pat Lambie were cut short when referee Bryce Lawrence correctly called de Villiers' scoring pass forward.
A double tackle from O'Connor and Rocky Elsom then bundled Spies into touch as the Springboks, who were now dominating possession and territory, cranked up the pressure.
Australia rode their luck when Cooper had a clearance charged down by Bismarck du Plessis and in the 61st minute they slipped behind for the first time when Steyn booted a drop goal.
Cooper's problems continued when he sent a chip straight into touch and moments later Lambie steered a drop goal wide.
Bodies were strewn across the pitch and the game had lost any structure.
But when Australia finally broke from their half, they won a penalty against Matfield for pulling down at the line-out and O'Connor made no mistake from long range.
A late assault from the South Africans followed, but this was the Wallabies' day.