Marko Stankovic (13') scored early for the hosts but Nikola Krcmarevic (61') manage to equalise in the second half as the teams shared the spoils. Kerala rose to fifth in the table while the Stallions moved off the bottom spot.
Pune City interim coach Pradhyum Reddy made two changes from the side that lost 4-2 against FC Goa. Vishal Kaith was replaced by Kamaljit Singh in between the sticks while Adil Khan returned to the XI in place of Ashique Kuruniyan.
The visiting team's coach David James effected three changes after their 2-2 draw against Jamshedpur FC. He brought in Cyril Kali and his super-subs from the last match, Seiminlen Doungel and Sahal Abdul Samad.
Lalruatthara, Keziron Kizito and Halicharan Narzary made the bench. Dheeraj Singh, too, continued as a substitute while Naveen Kumar got his third successive start in goal for Kerala.
The Blasters started on the front foot with CK Vineeth forcing Kamaljit into his first save in the 10th minute. The Pune custodian also had to deal with Slavisa Stojanovic's shot on target before the hosts got the lead against the run of play.
Stankovic left rival goalkeeper Naveen Kumar with no chance as he turned away from his marker and unleashed a powerful left-footer that found the top corner of the net in the 13th minute.
Emiliano Alfaro could have equalised at the 20th-minute mark but headed Stankovic's flag-kick wide despite being left completely unmarked in the box. Matej Poplatnik similarly headed wide at the other end minutes later.
Controversy followed towards the end of the half as Nikola Krcmarevic was seen struggling to bury the ball at the back of the net with Alfaro putting his body in the way before Kamaljit claimed the ball just in front of the goal line.
However, Alfaro did appear to handle the ball to prevent the ball from crossing the line - something that was missed by referee OP Thakur.
Kamaljit's had to save a deflected attempt from Samad after that as Pune were lucky to maintain their one-goal lead at half-time.
Alfaro missed a penalty for a second straight game when he hit the bar after Pune were given a soft penalty. The Uruguayan made the best of the slightest of touches from Krcmarevic in his back and referee Thakur had pointed towards the spot about 10 minutes into the second half.
Kerala finally bagged the equaliser in the 61st minute when Krcmarevic blasted the ball past Kamaljit after a half clearance by Gurtej Singh.
Despite throwing only a few men in attack, Pune did manage to create some openings for themselves including Marcelinho's shot that caught a deflection from Alfaro but there would be no winner for either team.