Babar Azam fell one short of a maiden Test century after a farcical Azhar Ali run out as Pakistan put themselves well on course for victory over Australia in Abu Dhabi on day three.

Azhar threw his wicket away comically for 64 at Sheikh Zayed Stadium, Mitchell Starc zipping in a throw and Paine whipping off the bails as the number three casually chatted to Asad Shafiq out of his ground thinking he had struck a boundary.

There was also agony for Babar when he was dismissed for 99, but Pakistan should have the last laugh after declaring on 400-9 to set the tourists a highly unlikely 538 to win.

Usman Khawaja's magnificent century denied Pakistan in the first Test, but he was unable to open due to a knee injury on Thursday and his replacement, Shaun Marsh, fell cheaply as Australia were reduced to 47-1 at stumps.

Sarfraz Ahmed (81) earlier made a second half-century of the match, with Nathan Lyon taking 4-135 on a gruelling day for Australia.

Lyon struck in the sixth over of the day with a flighted delivery which deceived an advancing Haris Sohail, who was stumped by Paine.

Azhar followed in bizarre fashion soon after to leave Pakistan 160-4, but Babar and Shafiq capitalised on an excellent batting surface in a stand of 75.

Shafiq was twice dropped by Marnus Labuschagne at short leg off Lyon before the all-rounder dismissed him for 44 in the afternoon session.

Babar had brought up his half-century and continued to tick along effortlessly, launching Labuschagne for six over long-off before Sarfraz did the same to Lyon straight after sweeping him to the boundary.

Peter Siddle rattled Sarfraz on the helmet, but the skipper brought up his second half-century of the match and Babar was on the brink of a first Test hundred when he was trapped leg before by Mitchell Marsh.

Babar reviewed, in hope more than expectation, but was sent on his way after hitting three sixes and another six boundaries in an excellent knock, putting on 133 for the sixth wicket with Sarfraz.

Bilal Asif smashed Labuschagne's first ball after tea for a straight six, but he and fellow spinner Yasir Shah fell in the same Lyon over, much to the frustration of Sarfraz.

Sarfraz decided it was time to deal in boundaries, but missed out on a hundred again when Labuschagne snared him leg before and declared soon after trudging off.

Stand-in opener Shaun Marsh failed for the fourth time in the series, bowled by a peach of a delivery from Mir Hamza which nipped away and struck the top of off stump.

Aaron Finch and Travis Head prevented any further damage from being done, but Pakistan have two days to take the nine wickets needed to win the series.