Lydia Greenway hit an England record 80 not out, from 64 balls, to chase down 127 for seven with six balls to spare.
England had been in trouble when they fell to nine for three but a 65-run stand between Greenway, who survived a missed stumping on 10, and captain Charlotte Edwards set up victory.
Greenway deservedly completed the win with a angled sweep to move England into an unassailable 10-4 lead - four days after the men confirmed their 3-0 Test series win.
Victory was England's fourth in a row in the innovative series - when points have been awarded for each win - after the only Test was drawn and Australia won the opening one-day international.
England's chase immediately hit rocky ground as Heather Knight missed a Julie Hunter straight ball before Sarah Taylor was the first of two Sarah Coyte wickets in as many balls.
Taylor, who hit 77 in the first Twenty20, thumped a straight drive that Coyte somehow held onto with one hand before Danielle Wyatt was bowled next ball.
Greenway should have soon followed when she ran down the wicket and missed a swipe at Erin Osborne, only for wicketkeeper Jodie Fields to miss the ball.
It proved a decisive moment as Greenway took over, with the deftness of her angled shots behind the wicket the feature, in an Ashes-winning innings.
Australia built their target around opener Meg Lanning's 53-ball 60.
The right-hander brought up her half-century by lifting Jenny Gunn over the square leg rope, but was unluckily run out at the non-striker's end when Holly Colvin deflected Alex Blackwell's straight drive onto the stumps with the opener out of her crease.
England then applied the clamps in the final stages, claiming a team hat-trick from the first three balls of the last over.
Danielle Hazell had Blackwell caught in the deep before Fields was run out attempting a second.
Osborne then walked in front of a straight one to leave Hazell with the impressive figures of two for 11 from her four overs.
- Sports & Recreation
- Lydia Greenway