Australia had already secured the Ashes, going into Wednesday's match unbeaten in the points-based series with a 12-2 margin.
Heather Knight's side, though, came out on top at the County Ground, having made 139 for five after being put in to bat.
Opener Tammy Beaumont managed only five, while Danni Wyatt scored 20 from 19 balls, with Knight then run out for 23 and Natalie Sciver (five) also falling cheaply when she was caught at third man off a top edge.
However, Lauren Winfield hit a rapid 26 and Yorkshire's Katherine Brunt also ended the innings unbeaten on 25 to add 43 from the last four overs and help set a competitive total.
Brunt and Sophie Ecclestone – who took two in as many balls – then claimed three wickets each to restrict Australia's run chase, with an unbeaten 60 from Ellyse Perry not enough.
Australia opener Alyssa Healy had made 28 before she was the first of two wickets for debutant off-spinner Mady Villiers, who also had Ashleigh Gardner stumped for a golden duck in the same over.
Captain Meg Lanning was trapped lbw by Ecclestone for just two and the tourists always looked up against it after slumping to 45 for four inside 10 overs.
Brunt finished with three for 21 while Ecclestone, England's leading wicket-taker in the series, had figures of three for 22 from her four overs.