Shaw and Gill were dismissed for a duck while Agarwal managed to register just one run.
All the batsmen were dismissed by Scott Kuggeleijn and as a result, the side was reduced to 5/3 in the seventh over.
For the practice game, the two teams mutually decided that the visiting team will bat first in the three-day warm-up game.
In the ongoing practice match, Ajinkya Rahane played a knock of 18 runs, but Jimmy Neesham dismissed him in the 16th over, reducing India to 38/4.
Regular opener Rohit Sharma has been ruled out of the Test team due to an injury and in place of him, one of Shaw or Gill are likely to play in the first Test. India will take on New Zealand in the first match of the two-Test series, beginning February 21 at Wellington.