French International David Trezeguet gave the hosts an early lead with his 15th minute strike to bring the home fans to their feet.
Trezeguet took a volley from a spectacular ball delivered by John Goossens from the left wing to fire it into the goal.
But the cheer was shortlived as Kerala soon pulled up their socks to go full throttle and India U-23 forward Chinadorai Sabeeth equalised in the 41st minute.
This was Sabeeth's first goal in the league and the 23-year-old striker celebrated it in great style.
Attacks and counter-attacks continued from either end of the goal but the score remained 1-1 at half-time.
The break did not prove too good for the home team as Pune goalkeeper Emanuele Belardi of Italy walked off the field in the 50th minute and Churchill's Arindam Bhattacharya took charge at the post.
Kerala think-tank then came up with a substitution as Penn Orji replaced Brazil's Guilherme Milhomem Gusmao in the 61st minute.
Orji soon made it count when the Kenyan international scored in the 65th minute.
Iain Hume's spectacular pass from the right wing was safely taken inside the box by Orji and he perfectly shot it at the bottom right corner to give Kerala the decisive lead.
From then on Pune tried hard to comeback into the game but the away team proved to be strong with their defense.
Kerala next travel to Mumbai on November 2 while Pune visit Kolkata on November 7.
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