Middle-order batsman Misbah top scored with an unbeaten 71 for his maiden half-century in eight Tests. Tailender Mohammad Sami was the other not-out batsman at stumps with 20.
The pair added 68 for the unfinished ninth wicket, denying India success in the last session.
Veteran leg-spinner Kumble finished with 3-38 in his first Test as captain as Pakistan virtually lost the advantage of winning the toss on a good batting track at the Ferozeshah Kotla ground.
Kumble was superbly backed by left-arm seamer Zaheer Khan, who jolted Pakistan with two early wickets to finish with 2-36.
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Misbah alone applied himself remarkably well, hitting one six and five fours in his 204-ball knock. The pick of his shot was a straight six off part-time seamer Sourav Ganguly.
There was just one false stroke in Misbha's solid knock when he mistimed a pull off fast bowler Munaf Patel, but fielder Harbhajan Singh failed to hold the catch at mid-wicket. He was then on 69.
Pakistan were let down by their top-order batsmen on an easy-paced pitch as none could build a sizeable partnership. Yasir Hameed (29) and experienced Mohammad Yousuf (27) looked settled before they were dismissed.
The Indian bowlers called the shots in the opening two sessions, making the batsmen struggle for runs with a tidy line and length.
Zaheer did the early damage with two quick wickets in his opening spell, removing Salman Butt and vice-captain Younis Khan to send the tourists struggling at 35-2.
He struck in his third over when he bowled left-handed Butt (one) with a delivery that cut in sharply. He then had Younis (seven) caught hooking by Patel at fine-leg.
Kumble did not have to wait long for his first wicket as he deceived opener Hameed with a straighter one in his fourth over before accounting for Kamran Akmal (30) and Shoaib Akhtar (two).
Ganguly got a big wicket when he trapped prolific run-getter Yousuf leg-before in his first over after the lunchbreak and then Patel removed skipper Shoaib Malik for a duck.
Patel, who returned to the side after missing Test series in England and Bangladesh, had the Pakistani captain caught behind in his second spell. He was economical in the opening period, giving away 14 runs in seven overs.
The Pakistani batting continued to wobble as Kumble bowled Akmal and Harbhajan trapped debutant Sohail Tanvir (four) leg-before in his first Test in more than a year.
India went into the first match of a three-Test series with two spinners, Harbhajan and Kumble, and as many seamers, while Pakistan named three fast bowlers and one spinner in their playing eleven.
The hosts hardly felt the absence of a fifth specialist bowler as Ganguly kept the batsmen under control in his 12 overs.
Pakistan suffered a setback when fast bowler Umar Gul was ruled out of the match due to a back injury. He was replaced by Sohail Tanvir.