ATK's star signing Robbie Keane made his much-awaited ISL debut, coming in the 61st minute and orchestrated the team's goals but could not finish on the winning side.
After a lacklustre first half which saw both teams try hard to break the deadlock without much success, the home side came up trumps after a flurry of goals in the last 25 minutes.
In a contest of fluctuating fortunes, Chennaiyin were 1-0 and 2-1 up before the final minutes saw two strikes from either side with the home team coming up with the all- important goal in the 90th minute.
Jeje had scored the game's first goal in the 65th minute following some beautiful play by Chennaiyin.
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Jaime Gavilan took a short corner and immediately received the pass back from the far post. He swung his cross into the box where skipper Henrique Sereno jumped and headed it towards the goal. It ricocheted off the inside of the post for Jeje to put it back into the empty net.
It was Jeje's first goal of the season, vindicating coach John Gregory's faith in him as he stated during the press conference yesterday that the Mizoram marksman would score sooner rather than later.
Inigo Calderon put Chennaiyin ahead in the 84th minute with an assist from Jerry Lalrinzuala as the match got more exciting.
Five minutes later, Njazi Kuqi slotted home a reverse ball from Keane, past Karanjit, much to the delight of the ATK bench including the coach Teddy Sheringham.
The joy was shortlived as Jeje fired home as the clock ticked over to the 90-minute mark to send his teammates into raptures.
The three points sent Chennaiyin to the top of the standings with nine points from four games, including three wins.