The Australians, beaten by the same margin in Adelaide on Wednesday, were superior with bat and ball to cruise to victory.
The home side restricted South Africa to 101 for seven off their 20 overs and had few problems reaching 102 for three in 12.4 overs to wrap up victory.
The series now goes to a decider in Sydney on Sunday.
"That was as good Twenty20 bowling as I've seen from our boys, we bowled to the conditions really well," Australia skipper Aaron Finch said.
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The Proteas, who dominated the Australians in the Adelaide opener, were always under pressure after winning the toss.
Skipper JP Duminy played a lone hand topscoring with 49 off 51 balls with three fours and a towering six over the fence at the vast MCG arena before he was caught in the deep by Finch.
In the space of two overs, openers Quinton de Kock and Rilee Rossouw were both back in the changerooms.