Mohammad Rizwan’s side was dismissed for 133 as they were chasing a target of 148 runs. Pakistan lost the key wicket of Babar Azam on first ball of the second over at 12 runs while Sahibzada Farhan was removed in a quick session for five runs.
Rizwan could score 16 runs before he was dismissed by Spencer Johnson as the top order failed to take a strong start. Usman Khan smashed a fifty to help his side recover from pressure but he could not stay for long as he was removed by Johnson.
Irfan Khan made unbeaten 37 runs as no player from tail order could perform as Australia managed to clinch the series.
Earlier, Australia set a target of 148 runs after decided to bat first. Matthew Short made 32 runs while Jack Fraser McGurk scored 20 runs and Aaron Hardie made 28 runs.
Haris Rauf claimed 4 wickets becoming the joint-most wicket taker for Pakistan in T20 Internationals while Abbas Afridi took three debutant Sufyan Muqeem grabbed two scalps.
In first match, Australia beat Pakistan by 29 runs in the rain-hit seven-over opening game of the three-match T20I series at the Gabba in Brisbane on Thursday. Pakistan managed 63-9 in the allotted overs after Australia raced to 93-4 off the 42 balls they faced.
Earlier, bad weather delayed the start of play before Pakistan won the toss and opted to field first. After Naseem Shah and Haris Rauf removed the Australia opening batters for single digits, Glenn Maxwell hit five fours and three sixes in his breezy 19-ball 43.