Both players have been struggling with chronic injuries over the course of the series, which also involved Zimbabwe, with Morkel aggravating a rotator cuff tear in his right shoulder and Duminy battling with a left knee problem.
However the pair successfully completed their fitness tests, leaving South Africa to make just one change to their side with leg spinner Imran Tahir coming in for batsman Rilee Rossouw.
South Africa captain AB de Villiers won the toss and opted to bowl first under sunny skies, meaning his side will chase for the third successive game against Australia.
While South Africa won the first encounter by seven wickets, Australia clinched the second by 62 runs.
Australia also made one change, with James Faulkner replacing Kane Richardson.
Teams
Australia: Aaron Finch, Phillip Hughes, Steve Smith, George Bailey (capt), Mitchell Marsh, Glenn Maxwell, Brad Haddin (wkt), Mitchell Johnson, Mitchell Starc, James Faulkner, Nathan Lyon.
South Africa: Hashim Amla, Quinton de Kock (wkt), Faf du Plessis, AB de Villiers (capt), David Miller, JP Duminy, Wayne Parnell, Dale Steyn, Aaron Phangiso, Imran Tahir, Morne Morkel.