With the three-match contest locked at 1-1 and Pakistan eyeing their first ODI series win in Australia since 2002, skipper Mohammad Rizwan won the toss and sent in the hosts.
They proved no match for a high-quality attack led by Afridi (3-32) and Shah (3-54), with support from Haris Rauf (2-24).
Sean Abbott top scored with 30 before they were bundled out in the 32nd over for just 140.
Australia were without Steve Smith and Marnus Labuschagne, along with pace trio Pat Cummins, Josh Hazlewood and Mitchell Starc who are being rested ahead of the Test series against India.
For the third consecutive match Jake Fraser-McGurk and Matt Short opened the batting, desperate for runs after failing to make an impact at Melbourne and Adelaide.
But on a pitch suited to the quick bowlers Fraser-McGurk again flopped, nicking a swinging Shah delivery to wicketkeeper Rizwan on seven.
Aaron Hardie, promoted to three in place of Smith, lasted 13 balls for his 12 before being caught at slip off the dangerous Afridi.
That brought stand-in skipper Josh Inglis to the crease, but he too departed cheaply for seven, skying a Shah bouncer that Rizwan collected to leave Australia on 56-3 in the 11th over.
Rauf, who took 5-29 in Adelaide, then accounted for Short (22) before youngster Cooper Connolly, in only his second ODI, was forced to retire hurt on seven after a nasty blow to his hand.
The out-of-form Glenn Maxwell only survived two balls with Rauf bagging him for the third time this series, caught at point by Saim Ayub, while Marcus Stoinis added just eight to the score as Australia stumbled to 88-6 in the 21st over.
Abbott and Adam Zampa (13) shared a handy 30-run partnership before the tail was mopped up.
AFP
