Goa made a positive start with a Julio Cesar goal in the 24th minute. Second half strikes by Mohammed Rafi and Kervens Belfort capped off a superb comeback by Kerala as they registered their first away win of the season.
With the win, Kerala are fifth in the standings with eight points from six matches, Goa are placed at the bottom of the eight-team tournament with four points from as many matches.
Rafi dragged a shot wide in the 14th minute after a good lay-off by Belfort had set up the Indian striker on the edge of the box. Kerala's failure to make their early pressure pay was punished by Goa 10 minutes later.
A quality cross from the left by Richarlyson found Cesar in a good position at the far post. The Brazilian striker outjumped Josu Currais and rose highest to power in a header to make it 1-0 for the hosts.
Goa custodian Subhasish Roy Chowdhury was called into action again in the 35th minute when a Sandesh Jhingan flick-on from a Blasters free-kick looked goal-bound.
The Goa shot-stopper was alert to the danger and just managed to tip the ball over the crossbar to maintain his side's 1-0 advantage at the break.
Kerala found their equaliser right from the restart after Mehtab Hossain found Mohammed Rafique with space on the right. Rafique's dangerous low cross across Goa's six-yard box was met by Rafi's left foot to make it 1-1.
Cesar went close to restoring Goa's lead in the 54th minute with an effort from range that was fractions wide of Kerala's goal.
The Brazilian's next attempt forced Kerala goalkeeper Nandy into a save nine minutes later after a powerful free-kick from far out required the Indian goalkeeper's intervention low to his left.
Kerala had a huge opportunity of scoring the winner when striker Michael Chopra found the ball at his feet in the 80th minute. His shot was saved by Chowdhury.
Goa looked shaky in defence with the game approaching its climax. Defender Gregory Arnolin almost scored an own goal in the 83rd minute when an attempted header back to Chowdhury struck the frame of Goa's goal.
Belfort scored the winner a minute later for Kerala. The Haitian received a on the left flank before driving at Goa's defence and unleashing a thunderous effort from distance to make it 2-1 and settle the match.