Prithvi Shaw's 77 runs off 48 deliveries and Ruturaj Gaikwad's 30 runs helped India A, chasing 220, put up an opening stand of 82 runs for the Indian team. For Kiwis Logan van Beek scalped three conceding 46 runs while Jacob Duffy bagged two wickets.
In the first innings, New Zealand posted 173/8 on the board, with Glenn Phillips (69*), James Neesham (29), and Martin Guptill making notable contributions with the bat.
New Zealand were due to fly out of home on Sunday, but Santner - who was to lead the Kiwis during the T20I part of the series - will stay at home ahead of three T20I and three ODIS against Ireland later this month.
The New Zealand international has been involved in his country's Test squads over the past two years, and since the beginning of 2020, has taken 82 wickets in 28 matches.