The visitors levelled the series in a final-ball thriller at Johannesburg, where Warner and Glenn Maxwell starred in the nation's highest-ever successful T20 chase.
The results will buoy the 15-man squad as they prepare to depart for India, where Australia's World T20 campaign starts on March 18 against New Zealand.
The most pressing concern for coach Darren Lehmann is finalising his best XI.
Deciding which two of Watson, Khawaja and Aaron Finch to open with appears the decision that will trouble Lehmann and on-duty selector Mark Waugh the most.
Otherwise the side that played at Newlands is likely to face the Black Caps, with the possible exception of omitted Test spearhead Josh Hazlewood.
Lehmann will be stroppy about a handful of misfields his side committed in Cape Town, where Maxwell put down a dolly at deep midwicket.
But otherwise there were plenty of positives for the tourists, who have never won the World T20.
Nathan Coulter-Nile grabbed two wickets, again accounting for dangerous opener Quinton de Kock in the powerplay.
Legspinner Adam Zampa, who troubled the hosts with bounce as much as turn, was Australia's best bowler.
The Proteas were 68-1 after six overs when Zampa was first called into the attack.
The tweaker's tidy figures of 0-23 from four overs were a godsend for Smith, who fired with the bat after nervy knocks in Durban and Johannesburg.
It was a mix of classical and funky from the skipper, who used his trademark 'tweener shot to send a Dale Steyn yorker fizzing to the rope.
Smith brought about his own downfall in the penultimate over, when a scoop shot went awry.
Maxwell steadied with a six over the off-side fence, while Mitch Marsh brought up the winning runs to ensure there was no late twist.
South Africa were also sloppy in the field, with Watson dropped on 30 and 40 off the bowling of Tahir.
The series was essentially a selection trial for both sides.
However, a lively exchange between Warner and Proteas paceman Kagiso Rabada was a snapshot of the intensity that all three games were played at.
Meanwhile, Amla's career-best T20 knock was interrupted by a squirrel that scuttled across the field throughout the Proteas' dig.
"It's the first time I've seen a sporting event held up by a squirrel," Waugh said while commentating.
- AAP
