Australia 100 for 2 (Mooney 46) beat Pakistan 96 for 7 by eight wickets
The hosts used nine bowlers on Thursday night at Hobart's Blundstone Arena, restricting Pakistan to 96 for 7 and chasing down the target in 12.4 overs with eight wickets in hand.
Mooney returned to the top of the order after not batting in the first game of the series because of soreness, and hit 46 from 29 balls. She shared a 60-run opening partnership with skipper Meg Lanning to iron out most of the total.
The win clinches the three-game series for Australia, following their eight-wicket win in game one, with the final match to be played in Canberra on Sunday.
Lanning shared the ball around in Australia's final series ahead of the T20 World Cup in South Africa beginning in February.
Darcie Brown, Ashleigh Gardner, Jessica Jonassen, Grace Harris and Annabel Sutherland all chipped in with a wicket each.
Star allrounder Gardner, who earlier this week expressed her discomfort with playing on Australia Day, was one of just two players to bowl four overs.
Gardner, a proud Muruwari woman, said January 26 was a day of hurt and mourning for Indigenous people. Australia's squad attended a smoking ceremony and completed a walking tour of kunanyi/Mt Wellington in Hobart, and wore an Indigenous jersey, socks and wristbands for the match.
Megan Schutt, who took 5 for 15 in the first game, conceded 10 runs from her one over.
There was an awkward moment not long before the first ball, with the on-field sprinklers briefly coming to life.