The South Africans, who led 20-3 at halftime, finished first overall on the combined points table while New Zealand will play France in the other semifinal.
The Junior Springboks scored their third consecutive bonus-point win scoring six tries to two and are still unbeaten after earlier wins of 33-5 over Italy and 40-8 over Samoa.
Flanker Jacques Vermeulen started proceedings to give his team a 7-0 lead in the third minute, while in the 18th minute prop Ox Nche was on hand to take a final pass and dive over for the second try of the evening.
Flyhalf Brendon Thomson kicked the two points on offer from an acute angle to stretch the SA lead to 17-3, while right wing Khanyo Ngcukana ran in to score shortly after halftime and with Thomson converting SA was 27-3 in the lead after 49 minutes.
With Cameron Orr (prop) yellow carded for a repeated offence in the scrum, Thomson scored South Africa’s bonus point try after 61 minutes to take the score to 34-3.
Jason Jenkins, the No 4 lock, showed a mean burst of speed to outflank the cover defence and slide over in the left hand corner and score try number five (39-3).
Australia hit back with their first try through inside centre Duncan Paia’uau to cut the deficit to 39-8, but wing Leolin Zas try rewarded the excellent SA effort minutes later when he score under the posts (46-8).
The Aussie captain, Andrew Kellaway (left wing) scored out wide after Dan du Preez was yellow-carded for illegal play, leaving SA with only 13 players until the end of the match.