Pakistan, chasing 180 for victory, reached 140 for three in 37 overs to edge nearer to their first Test victory over the Australians in 15 years. A Pakistan win would also deny Australia an eighth straight Test win.
Azhar Ali was 47 not out and Umar Akmal was on two when the players left the field despite bright sunshine.
Left-arm fast bowler Doug Bollinger claimed the late wickets of Farhat, who was bowled, and Umar Amin for a duck. Both wickets fell caught behind with the score on 137 to give Australia a glimmer of hope.
Australia, skittled for just 88 on the opening day, fared better second time around.
Resuming at 136 for two on Friday, Steven Smith scored an enterprising 77 off just 100 balls between lunch and tea, with nine fours and two sixes, to boost Australia's hopes after Michael Clarke made 77 and captain Ricky Ponting 66. But their first innings may ultimately have cost them.
Pakistan, who will hope to banish the painful memory of Sydney in January when they were bowled out for 139 when chasing 176, began their run chase nervously.
Farhat, who was dropped by Shane Watson at first slip, raised his half-century with a square cut off a short and wide Johnson delivery for one of his nine boundaries.
AUSTRALIA (I Innings) 88 all out
PAKISTAN (I Innings) 258 all out
AUSTRALIA (II Innings, O/n 136/2)
Watson b Amin 24
Katich b Aamer 11
Ponting c K Akmal b Aamer 66
Clarke c K Akmal b Asif 77
Hussey c U Akmal b Aamer 8
North b Aamer 0
Paine c Ali b Kaneria 33
Smith b Gul 77
Johnson lbw Asif 12
Hilfenhaus c U Akmal b Kaneria 17
Bollinger (not out) 0
Extras (B-4, LB-10, W-2, NB-8) 24
Total (all out, 95.3 overs) 349
Fall of wickets: 1-15, 2-55, 3-144, 4-158, 5-164, 6-217, 7-246, 8-283, 9-320.
Bowling: Aamer 27-6-86-4, Asif 26-4-83-2, Gul 15.3-1-80-1, Amin 6-1-12-1, Kaneria 21-2-74-2.
Pakistan (II Innings)
Farhat b Bollinger 67
Butt c Clarke b Hilfenhaus 13
Azhar (batting) 47
Amin c Paine b Bollinger 0
U Akmal (batting) 2
Extras (lb-6, nb-5) 11
Total (for 3 wkts, 37 overs) 140
Fall of wickets: 1-27, 2-137, 3-137.
Bowling: Bollinger 8-1-37-2, Hilfenhaus 6-1-16-1, Johnson 9-1-39-0, Watson 5-1-18-0, Smith 9-2-24-0.