Ahmed Shehzad (22) and Azhar Ali (16) were at the crease as Pakistan increased their lead to 189 runs at Dubai stadium.
Earlier, Australia were bowled out for 303 in their first innings, conceding a big 151-lead to Pakistan, who had made 454 in their first knock.
Opener David Warner scored 133 while Chris Rogers made 38 and Mitchell Johnson 37.
Debutant leg-spinner Yasir Shah took 3-66 while paceman Rahat Ali (2-55) and left-armer Zulfiqar Babar (2-81) also chipped in with useful contributions.
The second and final Test starts in Abu Dhabi from October 30.