Du Plessis was backed up by 82 from JP Duminy and 75 from Rilee Rossouw as South Africa scored 361-6 after being put in to bat by Australia.
Top-ranked Australia was bowled out for 219 in less than 38 overs, with only half-centuries from David Warner (50) and Travis Head (51) to show from its batting lineup.
South Africa leads the five-match series 2-0 after winning the first game by six wickets.
Wayne Parnell took 3-40 for the best figures for South Africa. Australia gave two fast bowlers, Joe Mennie and Chris Tremain, their ODI debuts.