Cameron White steered the Australians home with an unbeaten 41 off 31 balls to pip the Proteas in a tense decider at Sydney's Olympic Stadium.
The Australians had restricted the South Africans to 145 for six off their 20 overs after winning the toss, but needed 19.5 overs to get the winning run off White.
Australia took the series 2-1 after losing the opening game in Adelaide by seven wickets then claiming the next in Melbourne by seven wickets and winning here.
"Credit to our bowlers again, chasing 140-odd on that wicket you would be pretty comfortable most times so I'm just glad we got over the line at the end," said man-of-the-match White.
More From This Section
"I thought we bowled well at the back end of their innings and it's nice to be making runs so that's my job and keep doing it hopefully."
Giant all-rounder David Wiese captured three for 21 and spinner Robin Peterson took three for 28 to lead the South African attack.