Shoaib Akhtar had opener Aakash Chopra plumb in front in the seventh over for five and two balls later captain Rahul Dravid was run out without facing a ball to plunge India into crisis.
Multan triple centurion Virender Sehwag was batting on eight at the break.
Pakistan's first innings folded at 489, 73 minutes after the lunch break in reply to India's 287. The Pakistani tail frustrated the visitors who, after claiming four wickets in the first session, saw the last three wickets add 103 runs.
Rookie middle order batsman Asim Kamal struck a timely 73 that came off 141 balls with seven fours and three sixes to help Pakistan stretch the lead.
He added 46 runs for the eighth wicket with Akhtar (19) before stitching another 38 for the ninth with Umar Gul (14).
Resuming at 355 for three, Pakistan lost skipper Inzamam-ul-Haq without adding any run to his overnight score of 118, leg before wicket to Irfan Pathan in the first over of the day.
Lakshmipathy Balaji had Yousuf Youhana caught behind for 72 before Kamran Akmal played across to Pathan and was rapped on the pads and Mohammad Sami inside edged an innocuous delivery from the same bowler on to his stumps as four wickets fell for 31 runs.