South Africa are seeking their first ODI series win in Australia since 2009, while the home team are desperate to keep their momentum going ahead of the arrival of India for a three-format tour.
A defiant 22 by tail-ender Adam Zampa helped Australia to a defendable total, and pacemen Mitchell Starc, Josh Hazlewood and Stoinis combined to reduce South Africa to 68 for four.
The series is all square with the Proteas winning the opening game by six wickets and Australia snapping their seven-game losing streak to clinch the second by seven runs.
The happy outcome on Sunday of a 2-1 one-day global series triumph in Australia will be deemed suitable ammunition by the Proteas' brains trust - even with home challenges against Pakistan and Sri Lanka still to come - to run with it for the foreseeable future.
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The visitors were asked to bat first by the hosts.
Mitchell Starc did the damage, bowling a flawless line and length, with de Kock getting a tickle on the ball and wicketkeeper Alex Carey taking the catch.
However, Pretorius swung the game back in South Africa's favour by dismissing Marsh in the next over, when the left-hander looked to whip one towards the leg side but ended up skying it to Heinrich Klaasen at wide long-on.
But Du Plessis eventually indicated for the review though he was reminded that technically Miller had to provide the signal.
Du Plessis and David Miller shared a 78-run stand before the skipper dragged Pat Cummins onto his stumps for 47.
Australia's woes were compounded when Aaron Finch soon followed him back to the pavillon.
Carey supported Marsh as he made his sixth one-day ton in 98 balls, with six fours and four sixes, before he was caught at deep midwicket and hope began to evaporate.