Pujara's loss left the hosts' middle order exposed at 100 for 3 but captain Virat Kohli and Ajinkya Rahane stabilised the innings with an unbeaten 48-run partnership to take them to 148-3 at the break.
Santner delivered a good length ball which Pujara opted to play from the back foot. He stepped back but didn't go across far enough towards off stump. The left-arm orthodox action of Santner did the rest, taking the ball away from the right-hander and threading the narrowest of apertures to hit his target.
This was arguably Santner's best spell in the series as his confidence grows on Indian surfaces.
The match plot took a more predictable direction at the start.
Conspiracy theorists will froth over the fabled 'commemorative coin' used to conduct tosses in India, as Virat Kohli won his seventh consecutive effort at home and (drumroll) decided to bat. India reached 75-2 at lunch.
It's hardly Kohli's fault visiting captains keep calling incorrectly because he's not flicking the coin. The skipper masked his euphoria by whooping and fist pumping in front of an Indore crowd experiencing test cricket for the first time at the venue.
In those seven toss wins - which includes this match - India have won five of the tests. The other was washed out.
The hosts accelerated to 26-0 from four overs after initial delays to the start. One was for a change of ball, ridiculously for the second delivery of the game, and the other hold up was sightscreen movement issues as the Indore organisers experienced stage fright.
Captain Kane Williamson, returning to the side after recovering from his viral illness, changed tack and brought on Jeetan Patel. Williamson was asked in the captain's press conference when he thought the pitch would turn. What a priceless answer it would have been if he'd said "fifth over". Alas, he didn't, but significant damage to the pitch around the footmarks suggests spin will dominate.
Patel bowled four relatively good length balls which Murali Vijay defended. He went to clip the fifth through the legside, intending to ease it past Tom Latham at short leg. In a venus flytrap move which would leave Mr Miyagi beaming, Latham snaffled the ball as it bobbled up his right arm. It was just reward for the hours he spends taking catches in similar fashion each practice.
The Black Caps' jubilation disguised relief, given India's comfortable start.
Boult removed Gambhir lbw in the 20th over to make it 60-2.
The shock in the New Zealand ranks was the decision to opt for all-rounder Jimmy Neesham over Neil Wagner in their XI. No one has shown more heart for the national cricketing cause in recent tests than Wagner, who is poised on 99 test wickets, one shy of equalling Sir Richard Hadlee as the fastest New Zealander to 100 in 25 tests.
Selection decisions shouldn't be based on such statistics, however, they are a gauge of Wagner's impact and highlights how well he has performed under the burden carried as a first-change bowler often toiling in unenviable conditions without a new ball.
The pressure goes on Neesham to prove he was a better selection. It was hardly Wagner's fault New Zealand lost the opening two tests. The onus should be on the top seven - with Martin Guptill, Ross Taylor and BJ Watling averaging less than 20 for the series - to deliver accountability rather than needing another all-rounder option as batting insurance.
Perhaps it's simply the last roll of the dice in an effort to deliver New Zealand's first victory away against India in 28 years.
