Santner clinched seven Indian wickets for 53 runs in 19.3 overs.
Allrounder Ravindra Jadeja was the top scorer for India with 38 runs from 46 balls at the fag end of the innings.
Yashasvi Jaiswal and Shubman Gill slammed 30 each in the Indian total.
India bowled out New Zealand for 259 on Thursday.
Washington Sundar had picked 7 wickets for 59 runs for India.