The tourists resumed on 113 without loss in response to 454, with Warner the dominant partner in a first-wicket stand with Chris Rogers that would see him bring up three figures for the third consecutive innings.
But the powerful opener received scant support, with no other Australian batsman passing 50 as Pakistan wrapped up their opponents' innings for 303.
Rahat Ali (2-55) found reverse swing to give Australia early problems, while spin duo Yasir Shah and Zulfiqar Babar impressed with 3-66 and 2-81 respectively before Pakistan openers Ahmed Shehzad and Azhar Ali progressed to 38 for nought - a lead of 189 - before bad light brought a premature close.
Rogers was uneasy against the movement Rahat produced through the air and the veteran chopped a delivery angled back into him onto his stumps to fall for 38, thus ending his 128-run partnership with Warner.
If anything, Alex Doolan was even more uneasy against the left-arm seamer, scoring a scratchy five from 34 deliveries before an ill-advised attempt to break the shackles resulted in him being run-out by Rahat from mid-on.
Australia captain Michael Clarke lacked his customary poise against slow bowling and was pouched for just two at short leg by Azhar off slow left-armer Babar.
Warner and Steve Smith threatened a recovery with a 48-run partnership but Yasir struck decisive blows either side of lunch as the latter sliced to backward point for 22 and the centurion's contribution concluded on 133.
It was a beautiful piece of bowling as Yasir deceived Warner with a quicker ball from around the wicket to disturb the batsman's stumps and leave Australia 207-5.
Brad Haddin counter-attacked to match Smith's score and debutant Mitchell Marsh made 27 but, frustratingly for the tourists, neither could produce an innings of substance.
Haddin played on as Imran Khan (1-41) enjoyed success with the second new ball before Marsh, having shown greater aptitude against spin than many of his team-mates, played around a Babar delivery to be trapped lbw.
Aside from a typically gutsy 37 from Mitchell Johnson there was little else to recommend from the Australia tail, who were then unable to find the breakthrough they sorely needed with the ball in the 13 overs available before the close.
Shehzad has an unbeaten 22, while Azhar - promoted to open after Mohammad Hafeez sustained an ankle injury in the field - is 16 not out on the back of a first-innings half-century.