Mitchell Marsh struck 39* to get Australia home in a chase of 146 to secure Australia's No.1 ranking in T20Is.
With usual captain Eoin Morgan missing after dislocating his finger in the previous match, Moeen Ali stepped up as captain, though it was Aaron Finch who won the toss and he elected to insert England.
Some tight bowling up front from Mitchell Starc and Josh Hazlewood was rewarded with the wicket of Tom Banton – who had moved back up to open with Jos Buttler having left the bio-secure bubble.
The visitors had to wait until Adam Zampa's introduction for their next wicket, but he dismissed Dawid Malan and Sam Billings within his first two overs to halt England's progress even as Jonny Bairstow began to score more freely and reached his fifth T20I half-century.
Australia's other spinner, Ashton Agar, was the man to end Bairstow's innings, taking a good catch off his own bowling after making a lot of ground to get under the opener's top-edged pull shot.
Moeen and Joe Denly managed to provide some late impetus and boosted England up to a challenging if slightly below-par 145/6.
Australia's reply got off to flying start as they picked up 16 runs from Jofra Archer's opening over, including a huge six over square leg by Matthew Wade – in the side in place of Alex Carey and opening with David Warner also sitting the game out.
Wade fell to Mark Wood but Marcus Stoinis made sure to continue the opener's work as he put on 39 runs with Finch before being caught in the deep off Tom Curran.
With 60 required from the last 10 overs and eight wickets in hand, Australia looked to be cruising to victory. But Adil Rashid sent Glenn Maxwell and Finch packing in one over before taking a low return catch off Steve Smith to leave the visitors five down and leave England wondering if they could repeat their feats from the first match of the series.
Mitchell Marsh hit a 36-ball 39* though to ensure that their winning position was not wasted, putting on an unbroken 46-run stand with Agar to get Australia over the line with three balls to spare.
The result means that despite England taking the series 2-1, Australia remain top of the MRF Tyres ICC Men's T20I Team Rankings.
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