Gambhir hit 123 while captain Pujara was unbeaten on 139 at the end of the second day. At stumps, India A were 334/3 in 95 overs. The hosts lead by 66 runs.
Left-handed Gambhir, who is aiming to make a comeback to the national side, batted for 236 balls. He scored 11 boundaries. Pujara has so far scored 15 fours in his 228-ball stay at the wicket.
Gambhir and Pujara had a 207-run partnership for the second wicket. Virender Sehwag was dismissed for 38.
West Indies A lead the three-match series 1-0 after having won the first match in Mysore.
West Indies A 268 Vs India A 334/3 in 95 overs (Cheteshwar Pujara 139 batting, Gautam Gambhir 123, Virender Sehwag 38).