Australia's Damien Martyn scored 142, his sixth Test century of 2004, before Pakistan suffered a spectacular top-order batting collapse on the third day of the second Test at Durban on Tuesday.
Pakistan reached 85 for five in their second innings at the close of play to lead by 47 runs.
The not out batsmen were Mohammad Sami on eight and Shoaib Malik on 11.
Martyn's patient innings of more than six hours lifted Australia's total from 171 for five to 379 all out at tea in reply to Pakistan's 341, which included 111 from acting captain Yousuf Youhana.
Martyn put on 59 for the sixth wicket with Adam Gilchrist (48) and 93 for the eighth wicket with Jason Gillespie (50 not out).
Pakistan paceman Shoaib Akhtar (5 for 109) claimed his second five-wicket haul of the series and leg spinner Danish Kaneria was also a constant threat, taking five for 125 from 39.3 overs.
DEPLETED ATTACK
With Australia resuming on their overnight score of 203 for five, Pakistan had been aiming to snatch a big first innings lead.
The touring side's depleted bowling attack removed Shane Warne (10) and Gilchrist in the first session.
Martyn then combined brilliantly with the long-haired fast bowler Gillespie, who hit four fours and one six in two-and-a-half hours to score his second career Test half-century.
The 33-year-old Martyn is the second-leading scorer in Test cricket this year with 1,353 runs, behind team mate Justin Langer's 1,476. South Africa's Jacques Kallis is third on 1,278.
Martyn took almost five hours and 189 balls including seven fours to reach his 11th Test century, pushing a ball from Sami to mid-wicket and jogging through for a single with both arms raised.
The Western Australia right-hander, who made 100 not out in Australia's 491-run win in the first Test in Perth, was eventually trapped leg before wicket by Kaneria after hitting 12 fours, leaving the hosts on 347 for eight.
Shoaib then claimed his fifth wicket when he had Michael Kasprowicz caught in the gully for four and Glenn McGrath fell soon after to Kaneria for one.
Buoyed by their first innings advantage of 38, Australia's new-ball attack tore through Pakistan's top order.
McGrath removed Salman Butt for a duck in the opening over and Yasir Hameed for 23 after Imran Farhat had been caught at deep square leg off Jason Gillespie for five.
Leg spinner Warne had Youhana caught at silly point for 12 at 60 for four and Younis Khan (23) fell eight runs later to the bowling of Kasprowicz after a bizarre attempt at a pull shot.
Pakistan medium-pacer Abdul Razzaq was taken to a Melbourne hospital complaining of breathing difficulties on Tuesday and did not take the field.
Off-spinner Malik did not bowl after a report from the University of Western Australia recommended the all-rounder undergo remedial work on his bowling action. Malik batted at number six despite a hand injury.
Both teams observed a minute's silence before the start of play on Tuesday for the victims of the tsunami waves which killed more than 24,000 people across Asia.
Pakistan's regular skipper Inzamam-ul-Haq is not playing in the second Test because of a back injury.
Scoreboard:
Pakistan first innings 341 (Yousuf Youhana 111)
Australia first innings (203 for five overnight)
J.Langer c Imran Farhat b Danish Kaneria 50
M.Hayden c Shoaib Malik b Shoaib Akhtar 9
R.Ponting C Shoaib Malik b Shoaib Akhtar 7
D.Martyn lbw b Danish Kaneria 142
D.Lehmann c Yasir Hameed b Shoaib Akhtar 11
M.Clarke c Shoaib Akhtar b Danish Kaneria 20
A.Gilchrist c Mohammad Sami b Danish Kaneria 48
S.Warne c & b Shoaib Akhtar 10
J.Gillespie not out 50
M.Kasprowicz c sub (Naved-ul-Hasan) b Shoaib Akhtar 4
G.McGrath lbw b Danish Kaneria 1
Extras (nb-19, w-5, lb-2, b-1) 27
Total (all out, 99.3 overs) 379
Fall of wickets: 1-13 2-32 3-122 4-135 5-171 6-230 7-254 8-347 9-368
Bowling: Shoaib Akhtar 27-4-109-5 (nb-10, w-2), Mohammad Sami 23-2-102-0 (nb-7, w-1), Abdul Razzaq 7-0-27-0 (nb-2), Danish Kaneria 39.3-5-125-5 (w-2), Imran Farhat 3-0-13-0.
Pakistan second innings
Salman Butt c Kasprowicz b McGrath 0
Imran Farhat c Martyn b Gillespie 5
Yasir Hameed c Gilchrist b McGrath 23
Younis Khan c Hayden b Kasprowicz 23
Yousuf Youhana c Ponting b Warne 12
Shoaib Malik not out 11
Mohammad Sami not out 8
Extras (lb-1, b-2) 3
Total (for five wickets, 34 overs) 85
Fall of wickets: 1-0 2-13 3-35 4-60 5-68
Bowling: McGrath 9-1-25-2, Gillespie 5-2-10-1, Kasprowicz 10-2-30-1, Warne 10-4-17-1.
