The hosts resumed their first innings on 228 for six and advanced to 262 before losing their final four wickets for only 14 runs. They finished 276 all out to earn a first-innings lead of 45.
Openers Salman Butt - who went on to make 67 - and Yasir Hameed made a solid start for Pakistan, putting on 71 for the first wicket.
Hameed (36) was the only man to go between lunch and tea when he became the first of Anil Kumble's three victims thanks to a brilliant catch at silly-point by VVS Laxman.
Younus Khan departed soon after lunch for 23, trapped leg before wicket playing across the line to Kumble.
Mohammad Yousuf made a swift 18 before offering a caught-and-bowled opportunity to Harbhajan Singh and Kumble struck again when he induced an outside edge from Butt which was snapped up at first slip by Rahul Dravid.
Pakistan skipper Shoaib Malik also came and went before the close, bowled off an inside edge by Harbhajan for 11.
Misbah-ul-Haq - after being dropped on one by Wasim Jaffer - was 29 not out at stumps alongside Kamran Akmal (21).
Earlier, Laxman and skipper Kumble took the India total past Pakistan's first-innings score of 231 in the second over of the day.
But with India at 262, their 54-run partnership was finally broken when a Danish Kaneria delivery hit the shoulder of Kumble's bat, popping up nicely for Younus to take an easy catch at first slip.
Kumble's dismissal sparked a late collapse as the final three India wickets went cheaply.
Harbhajan faced only five deliveries, scoring one run, before his leg stump was removed by Sohail Tanvir.
Zaheer Khan hammered Kaneria for a six over long-on but perished for nine on the next delivery when he lofted the ball to mid-off, where Shoaib Akhtar took a fine catch.
Kaneria picked up his fourth wicket of the innings with the next ball, dismissing Munaf Patel lbw for a duck, leaving Laxman stranded on 72 as the Indians were dismissed for 276.
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