The hosts broke the deadlock in the first minute through Jackichand Singh. Ferran Cormonias scored a brace (52, 81') in the second half to seal the result.
Goa coach Sergio Lobera put his faith on Naveen Kumar in between the sticks for the second successive game and Edu Bedia replaced Hugo Boumous in the starting lineup.
ATK coach Steve Coppell replaced both Pronay Halder and Manuel Lanzarote with Kalu Uche and Hitesh Sharma in the first team.
Goa scored from their very first move as Jackichand found the back of the net from a Ferran Corominas cut-back from the right flank.
Hosts' skipper Mandar Rao Dessai got the better of Pritam Kotal on quite a few occasions to put in delightful crosses into the box. One of those threatened to go in but Corominas' touch sent the effort inches wide of goal.
Arindam then stood his ground to thwart Corominas' effort on goal after the Spaniard skipped past Arnab Mondal in the 20th minute.
Minutes into the second half, Bedia found Corominas to his right and the striker set Mandar up for a shot. Arindam dived to his left to keep it out but Corominas was at hand to slot in the rebound.
Ricky Lallawmawma fouled Corominas inside the box and conceded a penalty in the 81st minute. Corominas scored from 12 yards to take his goal tally to 13, overtaking NorthEast United's Bartholomew Ogbeche (12) in the Golden Boot race.