Habana, South Africa's record tryscorer, touched down in the 28th, 60th and 78th minutes while Zane Kirchner and Francois Louw also crossed as the Springboks maintained their 100 per cent record against Australia at Loftus Versfeld with a sixth win out of six.
The remainder of the home side's points came from the boot of scrum-half Ruan Pienaar, who converted three of the five tries, as South Africa earned a second victory in five matches to lift them into second place onto 12 points.
They are four points behind unbeaten leaders New Zealand ahead of the All Blacks' clash in Argentina.
Australia, whose points today came from an unconverted second-half try from Mike Harris and a Kurtley Beale penalty, are third in the standings on eight points after slumping to their third loss.
The Wallabies were badly hit by injuries in the defeat, though, and used all seven substitutes during the match before playing the final nine minutes with just 14 men.