Cedric Hengbart put the visitors into the lead in the third minute of the match before Mohammed Sissoko equalised for the hosts in the 69th at the Balewadi Sports Complex here.
Kerala got off to a flying start, Hengbart scoring the fastest goal of the ongoing edition of the tournament so far in 2 minutes 12 seconds.
Hengbart smashed in from close range after receiving the ball from a corner.
Pune's first chance came in the 15th minute but Tato volleyed the ball wide. They came closing in again three minutes later. But Traore's header missed the target.
Traore wasted another opportunity in the 40th minute when Jesus Tato provided an excellent delivery from the right but the header, under a challenge from Hengbart, sailed wide.
Pune continued with their attacks in the second session, hunting for the equaliser and it was Traore who went close again. A weak back-pass from Josu was cleared just in time by Kerala Blasters goalkeeper Sandip Nandy before Traore could pounce on the opportunity. When Traore finally headed the ball inside the nets, he was flagged offside.
Pune, however, were not to be denied the equaliser in the 68th minute. A cross from Jonatan Lucca saw Sissoko take a shot at goal which deflected off Hughes and sneaked past Nandy.
The draw meant Pune picked up their first point at home after losing two matches in a row. They now have four points from four matches, while Kerala Blasters have five points from five matches and are unbeaten in three games.