Australia needed 130 to win from 12 overs and were 30-3 from 3.5 overs as rain forced the players off the field for the third and final time.
England captain Jos Buttler said his team was building well for the T20 World Cup, having won the three-game series 2-0.
“We’ve made some good strides in Pakistan and we came here (Australia) and continue that form,” Buttler said.
It was a disappointing end to the game, the last official game for both teams before the World Cup, which starts on October 22.
After being sent off by Australian captain Aaron Finch, Buttler hit 65 from just 41 balls while England reached 112-2 in their 12 overs.
Australia, already trailing 2-0 in the three-game series, then needed 130 to win based on the Duckworth-Lewis method.
Match abandoned in Canberra.We win the series 2-0!🇦🇺 #AUSvENG 🏴 https://t.co/wU95GcMkVd
— England Cricket (@englandcricket) 1665746784000
And they got the worst possible start when Chris Woakes had Finch and number three Mitchell Marsh catch with the first two balls of the game to stun the home side.
He then ejected Glenn Maxwell in the third over, putting the Australians in big trouble 17-3 before rain forced an early end.
Finch previously won the toss and opted to field, with Australia themselves making the perfect start as Josh Hazlewood caught Alex Hales on the first slip in just the second left.
Buttler and Dawid Malan looked at ease and started to accelerate after a slow start, but shortly after the first rain delay Malan made a mistake in an attempted slog from Pat Cummins and was captured by Marsh halfway through for 23.
A second rain delay caused the game to be shortened to 12 overs each, and Buttler came out firing and shot 22 runs from the 11th over to help set up a challenging total.
Woakes’ brilliant opening spell made that goal unlikely and an Australian defeat seemed to be saved by the rain.
“It was really hard to stop the (English batters) and give them credit, they outsmarted us,” said Finch.