Pune pulled ahead early in the first half through Konstantinos Katsouranis but Chennai restored parity after the break when John Valencia scored.
With the draw, Chennaiyin FC went level on points with leaders Atletico de Kolklata at 12 points from seven matches but stayed in the second spot having an inferior goal difference to the table-toppers.
Pune improved to 11 points from seven matches but remained in the third spot ahead of fourth-placed Mumbai City FC. The home team went ahead early in the match through Katsouranis, who scored in the ninth minute. Israil Gurung sent in a lovely ball from the right wing and Kostas converted the accurate pass with great precision.
Chennai got a chance to get back on level terms quickly when they were awarded a penalty in the 16th minute.
Defender Daniele Magliocchetti gave away the penalty and was shown the yellow card when he committed a foul inside the box. Tournament's leading scorer, Elano, with eight goals, surprisingly blew that opportunity. His shot went wide after hitting the woodwork.
Chennaiyin went into the break trailing 0-1 but came back into the contest after the breather. After threatening to score on several occasions, forward Valencia finally netted in the 58th minute.
Balwant Singh provided a perfect pass into the box and Valencia netted with a calm and stylish finish. With the scores tied at 1-1, both teams launched attacks in search of what would have surely been the winning goal but all their efforts proved futile.