Chennaiyin arrived here on the back of two successive victories against FC Goa and NorthEast United and the defending champions appeared good enough to continue with their winning run, thanks to a fine goal from Jeje Lalpekhlua in the 28th minute.
Pune City, however, rescued a point late in the game after Anibal Rodriguez scored from a free-kick in the 82nd minute at Shree Shiv Chhatrapati Sports Complex Stadium.
The draw left FC Pune City with just five points from their first five matches -- four of them home matches -- while Chennaiyin FC moved to the third spot with eight points.
The match marked the return of Pune coach Antonio Habas from a four-match suspension. Chennaiyin coach Marco Materazzi relegated Jeje to the bench for the last two matches but named him in the starting line-up on Sunday.
He was rewarded for his judgment as Jeje won a tussle with Pune defender Eduardo Ferreira for the ball and capped the move with a superb lob over an out-of-position goalkeeper Edel Bete.
Bete tried to backtrack and retrieve the situation but Jeje's lob had enough power to carry the ball into the net.
Chennaiyin were disciplined at the back, allowing very little room for Pune to have a clear look at the goal. The only time Pune managed to test their rivals was from a distance as Jonatan Lucca and Jesus Tato's efforts sailed just wide of the target.
In the second session, Chennaiyin had a great chance to kill the contest. Defender, Eli Sabia's long ball was picked up by striker Dudu Omagbemi and his close-range shot was parried by Bete in the 48th minute. The rebound fell kindly for Hans Mulder but he couldn't provide the finishing touches.
Just when it seemed Chennaiyin would become the first team in this edition of the tournament to notch a hat-trick of victories, Pune equalised from a neatly taken free-kick from just outside the box by Anibal Rodriguez in the 82nd minute.