The 31-year-old is looking to become the first rider in more than a decade to claim back-to-back titles in the five-day event.
Froome finished 27th in last year's prologue over the same course and went on to win the tour.
Stage 1 of the tour starts in Wangaratta on Thursday.
Froome's Team Sky team-mate Danny van Poppel set a new course record in winning the 2.1km individual time trial through the centre of Melbourne with a time of 2mins 32secs.
Three-time Tour de France winner Chris Froome finished 26th in the Herald Sun Tour prologue in Melbourne on Wednesday - the Briton's first event of 2017.