Carl McHugh had put ATK ahead with an absolute stunner in the sixth minute but the hosts, egged on by a vociferous crowd, hit back with two goals from new signing Bartholomew Ogbeche in the first half itself.
This is the second time that Kerala beat ATK in the ISL opener after having won 2-0 in Kolkata last season.
The game got off to an electrifying start with the visitors stunning the packed crowd early into the game. A free-kick was cushioned back for McHugh by Agustin Garcia Iniguez at the far post. The Irishman went on to slam a brilliant first-time volley with his left foot which gave Bilal Khan in the Kerala goal no chance whatsoever.
With the wind in their sails from an early goal, ATK continued to press Kerala relentlessly and fashioned several chances to double their lead, but couldn't finish them off.
A rattled Kerala were handed a lifeline when ATK winger Michael Soosairaj went down inside the box following a challenge by Sergio Cidoncha, but the referee waved away the protests and Kerala won a corner from the ensuing counter-attack, which produced the equaliser.
Ogbeche saw his looping header from the far post come back off the upright, only for Pronay Halder to pull down Jairo Rodriguez who was about to slot it in. The referee awarded the spotkick and Ogbeche made no mistake in beating Arindam Bhattacharja to lift the spirits of the home supprters.
The Men in Yellow started to enjoy more time on the ball following the equaliser and stormed into the lead just before half-time. Pronay failed to clear a low cross from Prasanth Karuthadathkuni and the loose ball was driven in smartly by a lurking Ogbeche.
Kerala continued their ascendancy in the second half as well, but failed to add to their tally.
( With inputs from IANS )