With David Warner rested, Marsh made hay in his first series as T20 captain with back-to-back half-centuries to help the Australians seal victory with a game to spare.
Travis Head then blasted 91 off 48 balls on Sunday as Australia completed the 3-0 whitewash in Durban.
Long-serving opener Warner is set to return for the five-match ODI series starting on Thursday, which selectors will use to refine Australia's line-up for the 50-over World Cup starting in India in October.
Marsh batted at number three against the Proteas but stand-in head coach Michael di Venuto said he was being looked at as an opening option.
"There's lots of options for us moving forward opening the batting," Di Venuto told reporters.
"You look at the World Cup – David Warner comes back into the mix, Mitch Marsh, Travis Head, they've all got good form recently, they can all put a case forward to open the batting at the World Cup.
"Tonight Trav (Head) was really good, he stood a lot stiller and reacted really well to the ball. He can hit all around the ground."
Di Venuto confirmed spinner Adam Zampa would be fit to bowl against South Africa in the ODI series after a neck strain ruled him out of the third T20.
Australia will also be bolstered by the return of pace bowler Josh Hazlewood and wicketkeeper Alex Carey for the ODI series, which starts in Bloemfontein.
One mainstay who will not feature in South Africa is Glenn Maxwell, who left the tour after a few days when his ankle suffered soreness stemming from a previously broken leg.
The all-rounder is no certainty to return for the start of the ODI series against India from September 22.
"I still want to play some part of that India series," Maxwell told Australian media.
"But I'm not feeling any pressure on it. The selectors and the staff have been brilliant with me as well.
"They don't want to put too much pressure on me to sort of set that date because they know they've got a bit of extra time before the World Cup."
