Kerala rode on goals from Duckens Nazon (7th minute) and Aaron Hughes (57th) to climb to the third spot in the standings. Anibal Zurdo managed to halve the deficit from a free-kick for Pune in the closing minutes of the match.
It was Kerala's fourth straight victory that put them level with second-placed Atletico de Kolkata on points but are behind on goal difference. Pune's chances of qualifying for the semis now appear slim after their latest setback.
It was Kerala's penultimate home match of the Indian Super League (ISL) season. And they were on the front foot right from the kick-off, keeping the Pune defence busy.
Kerala Blasters coach Steve Coppell made several changes to the team that got clobbered in Mumbai with marquee player Aaron Hughes back into the squad, alongside Kervens Belfort, Duckens Nazon, Mohammed Rafi and goalkeeper Sandip Nandy.
Pune made three changes to their side but, playing at home, Kerala started the match on the front foot.
Kerala's attacking front-men of C.K. Vineeth, Nazon, Mohammed Rafi and Kervens Belfort were interlinking well to cause trouble for Pune.
They duly went ahead in the seventh minute. Nazon made a solo run after intercepting a ill-timed form Pune defender Dharmaraj Ravanan and duly converted stroking the ball into the net away from the clutches of Pune goalkeeper Edel Bete.
Pune tried to fight their way back but Kerala were always in control of the proceedings.
A corner in the 57th minute was only partially cleared by Pune City and Vineeth chased it down on the left, sending a cross to the far post.
The Pune defence shockingly stood still, allowing Aaron enough time to rush and head home from point blank range.
The goal crippled Pune, who however managed to pull a goal back in stoppage time. A cleverly taken free-kick set up Anibal Zurdo, who blasted it on to the far post, past goalkeeper Sandip Nandy.
The goal, however, came too late and there was no time for Pune City to get anything out of the match.