Atletico de Kolkata midfielder Jewel Raja Shaikh clinched the club's second title after gliding the ball past Graham Stack.
Atletico de Kolkata midfielder Jewel Raja Shaikh clinched the club's second title after gliding the ball past Graham Stack to stun Kerala's packed Jawaharlal Nehru Stadium.
Cedric Hengbart failed to give title favourites Kerala a lead after hitting a straight shot that was booted out by goalie Debjit Majumder before Shaikh scored on the last penalty kick.
The teams had been locked 1-1 at the end of normal time.
Forward Mohammed Rafi's header in the 37th minute gave Kerala an advantage but it was followed by an equaliser from Henrique Sereno Fonseca.
The second half saw both teams largely playing a defensive game, with neither side getting a breakthrough.
Kolkata, co-owned by former Indian cricketer Saurav Ganguli, won the first season of the tournament in 2014 after beating the Blasters, which is co-owned by former team mate Sachin Tendulkar.
Kolkata, coached by former Spanish footballer Jose Francisco Molina Jimenez, finished fourth in the league table but qualified for the finals by defeating table toppers Mumbai City FC in the semi-finals.
Kerala, who have ex-English footballer Steve Coppell in charge, qualified for the finals by beating the Delhi Dynamos.
Last season's champions Chennaiyin FC bowed out of the tournament at an early stage after winning just three games out of 14.