Opening the batting along side skipper Hanuma Vihari (59), Gill scored his runs off 153 balls with the help of 13 boundaries and one six to help India A pile up 234/1 in 53 overs.
Middle-order mainstay Chesterwar Pujara was giving Gill company at the crease on 52 off 99 balls at the draw of stumps.
Earlier, New Zealand declared their innings at 386 for nine in 131.5 overs after the second day’s play was washed out on Saturday.
Daryl Mitchell remained unbeaten on 103 off 222 balls during which he struck 10 boundaries and a six.
Besides, Glenn Phllips made 65, while wicketkeeper Dane Clever scored 53.
For India, Sandeep Warrier (2/50), Mohammed Siraj (2/75), Avesh Khan (2/82) and veteran off-spinner Ravichandran Ashwin (2/98) shared eight wickets among them.
India A now trail New Zealand A by 152 runs with just a day’s play remaining.
New Zealand A 1st innings: 386 for 9 in 131.5 overs (Daryl Mitchell 103, Glenn Phillips 65; Sandeep Warrier 2/50).
India A 1st innings: 234 for 1 in 53 overs (Shubman Gill 107 not out, Cheteshwar Pujara 52 not out; Blair Tickner 1/71).