Pandita scored the late goal with a towering header.
Jamshedpur FC will now await the challenge of SC East Bengal at the Athletic Stadium on Tuesday
Sahal Abdul Samad scored in the 27th to draw level for the Yellow Brigade. It was the striker's fourth goal this season and third in as many games.
Kerala have been unbeaten in six games while Jamshedpur haven't lost their last two.
Jamshedpur moved to the second spot on the table with 12 points but would rue their missed opportunity to close the gap on leaders Mumbai City.
The Scottish midfielder scored all three of his goals in the first half.
Defending champions Mumbai are four points clear at the top with 12 points from five matches.
The win took Jamshedpur to the second spot as Bagan slumped to fifth place.
Greg Stewart (41') scored a goal of the highest order for the Red Miners while Bartholomew Ogbeche (56') equalised in the second half.
Nerijus Valskis was the hero as JFC jumped to the top spot.