Warner, who made 133, was dismissed third ball after lunch as Australia fumbled to 282-8 at tea on the third day at Dubai stadium, still trailing Pakistan's first innings total of 454 by 172 runs.
Mitchell Johnson (22) and Steve O'Keefe (four) were at the crease.
Debutant leg-spinner Yasir Shah (2-55) spun one sharply to bowl Warner, who by then had anchored the Australian innings in the first session.
It was the left-hander's ninth Test century -- third consecutive in as many innings -- which took Australia to 207-4 at lunch after Pakistan fought back in the extended two-and-a-half hour morning session.
Mitchell Marsh (27) and Brad Haddin (22) took Australia to 248-5 during their 42-run stand for the sixth wicket but Pakistan broke through with the new ball taken as soon it was due after 80 overs.
Debutant paceman Imran Khan had Haddin bowled off an inside edge while left-arm spinner Zulfiqar Babar had Marsh leg-before.