Sehwag smashed four fours, including two in a row off pace spearhead Chris Martin, to move to 29 after facing 46 balls at the Rajiv Gandhi Stadium in Hyderabad.
Gambhir, eager to get back among runs after a string of low scores, was 28 not out with four fours, helping India reach 62-0 at tea.
Earlier, Zaheer Khan (4-69) and Harbhajan Singh (4-76) claimed four wickets each to bowl out the tourists just minutes into the second session.
Zaheer struck in the third over of the day when overnight batsman Gareth Hopkins (four) was trapped leg before wicket.
The bowler earned a bigger scalp three overs later, dismissing first Test centurion Kane Williamson who was caught plumb in front as he tried to drive the ball to the leg-side.
Harbhajan took his first wicket of the match, trapping Daniel Vettori lbw when he was on 11, New Zealand slipping to 312-7 from the overnight 258-4.
Jesse Ryder (70) continued his fine form on Indian soil, reaching his fifth Test half-century with a pulled four over backward point off fast bowler Shanthakumaran Sreesanth.
The left-handed batsman, who made 103 in the drawn Ahmedabad opener, has scored all of his three Test centuries against India, including a career-best 201.
But his dream of scoring a big one again was shattered by Harbhajan who had him caught at first slip by Venkatsai Laxman, playing his first Test on his home ground. Ryder struck 10 fours in his 120-ball innings.
Harbhajan removed tailenders Tim Southee and Chris Martin to wrap up the New Zealand innings.
The third and final Test will be played in Nagpur from Nov 20-24.
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