Malan shared a crucial 92-run stand in Canberra with Moeen Ali (44) as England compiled 178-7 against a full-strength Australian attack.
Despite Mitchell Marsh hitting 45 off 29 balls and Tim David 40 off 23, the hosts fell short.
Sam Curran took 3-25 to ensure England won the three-match series 2-0 with a game left on Friday in a setback to the World Cup champions.
England hold their nerve to take an unassailable 2-0 lead 🤩Watch the #AUSvENG series LIVE on… https://t.co/0FZuB8IL77
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“Really satisfying win after losing the toss as well and setting a target,” said England skipper Jos Buttler.
“I think we showed great character and Malan played fantastically well to anchor the innings.”
Malan hit seven fours and four sixes in his 49-ball knock to rescue the visitors after they slumped to 54-4 in the ninth over.
Ali was also impressive after Australian captain Aaron Finch won the toss and chose to bowl, making five changes to the side that also lost by eight runs in Perth.
Pace spearheads Pat Cummins, Mitchell Starc and Josh Hazlewood, along with spinner Adam Zampa all returned for the hosts after being rested for the first T20.
Buttler fell to Cummins on 17, with Zampa holding a difficult high catch.
Alex Hales, who blasted 84 from 51 balls in Perth, lasted just seven balls for his four runs before holing out to David Warner off Marcus Stoinis.
Star allrounder Ben Stokes’ ordinary recent form continued, bowled by Zampa for seven, and when Harry Brook got an edge off Stoinis they were on the back foot at 54-4.
But Malan was rock-solid, expertly finding the gaps to reach his 14th half-century.
Zampa finally broke the partnership, tempting Ali into another big hit and he was caught on the ropes before a late flurry from Malan, who was out in the last over.
“We were really poor in the field, sloppy, dropped a couple of chances, especially when we had them four down in the first 10 overs,” said Finch.
England rested pacemen Mark Wood and Chris Woakes but they still found a way to restrict Australia.
Finch dropped down the order in recent matches, but returned to partner Warner for the first time since their Sri Lanka tour in the middle of the year.
But he never settled and again fell cheaply, out for 13.
Warner, who has been in form, followed three balls later for four to leave Australia struggling at 22-2 in the fifth over.
Glenn Maxwell’s recent poor form continued, out for eight, before Marsh and Marcus Stoinis put on a quick-fire 40-run partnership to keep them in contention.
Stoinis went for 22, followed by Marsh, with Australia’s fate resting with David and Matthew Wade. They needed 59 of the last five overs but were unable to deliver the fireworks required.