The left-hander was unbeaten on 133 for his ninth Test century -- third consecutive in as many innings -- to take Australia to 207-4 at lunch after Pakistan fought back in the extended two-and-a-half hour session due to Friday prayers.
Australia trail Pakistan's first innings total of 454 by 247 runs with six wickets intact.
Mitchell Marsh was the other unbeaten batsman on nought at the interval.
Warner saw Australia lose Chris Rogers (38), Alex Doolan (five) and skipper Michael Clarke (two) in the space of just 30 runs before he and Steven Smith (22) added 48 for the fourth wicket.
The left-hander had hit a century in each innings against South Africa at Cape Town in Australia's last Test in March this year.
So far he has hit 11 boundaries and two sixes in his 171-ball knock.
Australia, resuming on a strong position at 113-0, lost Rogers when he played on to seamer Rahat Ali.
Rahat was again in the scheme of things when his direct throw from the mid-on found Doolan short of his crease as he attempted a sharp single.
Smith helped Warner to take the score to 206 before he fell in the penultimate over before lunch, playing straight into the hands of point to give leg-spinner Yasir Shah his first wicket.
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