MORE: Collier denies Pietersen claims
The tourists held an unassailable 2-0 lead heading into the third and final game in Abu Dhabi, but left Pakistan with an unremarkable target of 232 - losing their way somewhat after reaching 102-2 from 22 overs.
Pakistan mounted a steady chase and, as their innings progressed, it looked increasingly likely that the match would go down to the wire.
James Faulkner and Xavier Doherty celebrate after winning the third ODI. Photo: Getty
A controversial call saw Zulfiqar Babar remain at the crease despite appearing to have been run out by James Faulkner in the 47th over, but Pakistan failed to make the most of that reprieve.
Sohail Tanvir was bowled by Glenn Maxwell as he swung for glory with two runs left for the win before Mohammad Irfan stepped up with four balls to face.
MORE: India-Windies clash abandoned early
However, the 32-year-old was unable to hit the required runs and was caught by Faulkner as he went for broke off Maxwell's final delivery - the Australian bowler posting a two-wicket maiden over to finish off.
The result sees Australia remain at number one in the ICC ODI rankings.
With the series victory out of their grasp, Pakistan rang the changes with captain Misbah-ul-Haq among those to miss out, while Australia chose to bat first after winning the toss.
Stand-in skipper Shahid Afridi (2-44 off 10 overs) led by example by claiming the key wickets of David Warner (56) and Maxwell (20) to disrupt Australia's rhythm.
Aaron Finch had already been caught for 18 by the time that Afridi took his double and Australia skipper George Bailey went for a duck after facing just three deliveries.
Steve Smith was the tourists' star performer with the bat, reaching his haul of 77 with the aid of only three boundaries.
Pakistan picked off the remainder of the Australian order with relative ease - Faulkner (33) the only other man to reach double figures - as Tanvir (3-40) delivered with ball in hand to restrict their opponents to 231-9.
The chase got off to a steady start for Pakistan, with Ahmed Shehzad (26) the first to fall with 56 on the board before Sarfraz Ahmed (32) followed six overs later.
Fawad Alam's dismissal for a duck proved controversial amid allegations Smith moved from his fielding position before the batsman had struck the ball, subsequently making the catch.
Australia arguably got lucky on that occasion, but they were given cause for concern soon after when Warner limped from the field after catching out Sohaib Maqsood (34).
Asad Shafiq top-scored with 50 for Pakistan before Afridi (6) came to the crease looking to lead his side to victory, but a wild and high strike was easily plucked from the air by Smith off Kane Richardson's delivery.
Confusion reigned in the closing stages when Faulkner appeared to have stumped Zulfiqar Babar (14 not out), who was inches short of the crease, but the officials decided against going to the third umpire and there did not appear to be any appeal from Australia.
Tanvir (10) subsequently smashed a Maxwell delivery for six to boost Pakistan's chances of snatching victory, but a blockbuster effort went awry in the final over as the bowler found the stumps.
The onus then fell on the incoming Irfan (0), but the experienced campaigner was unable to deliver as Pakistan fell agonisingly short of making the series result look a little less emphatic.