With the win, Kerala jumped up to the fifth spot in the standings with four points from as many matches, just above Pune who also have four points from four matches but are behind on goal difference.
FC Pune City's marquee player David Trezeguet put his team ahead early in the first half, only for Kerala to equalise just before the break through striker C.S. Sabeeth. Subsitute Penn Orji scored the winning goal for the away team.
The hosts found their stride early with Trezeguet scoring his first goal of the tournament. Fed by a spectacular ball delivered by John Goossens from the left wing, the Frenchman took a first-time volley to put his team ahead.
After the opening goal, Pune took control of the proceedings, stitching together good passes.
Kerala, on the backfoot and failing to create any meaningful attack, were forced to make a substitution in the 25th minute, injecting pace in the form of Ishfaq Ahmed in place of veteran Renedy Singh.
The change brought energy and purpose back in Kerala's game and they equalised in the 42nd minute.
Cedric Hengbart guided a well-taken corner by Stephen Pearson towards the goal for team-mate Sabeeth to put it in to go into the break level at 1-1.
And the visitors successfully carried forward the momentum gained after the equaliser into the second half, taking the lead in the 66th minute through substitute Penn Orji who came in place of Pedro Gusmao.
Orji's impact was telling. Iain Hume essayed a brilliant pass to Orji who converted it coolly to surge his team ahead four minutes after entering the field.
From then on Kerala, inspired by Orji, dominated the contest with the Nigerian coming close to scoring several times, but couldn't quite convert the chances that came his way.
But in the end they didn't have to rue the lost opportunities as they held on to the lead to collect their first three points.