Two goals, both from penalties by captain Manuel Lanzarote Bruno and one by Jayesh Rane, early in the opening half, stymied CFC's hopes.
ATK has 15 points from 10 matches after tonight's win and is fifth in the standings while the holders are down in eighth with five points from 10 games.
Isaac Vanmalsawma scored in the 88th minute to help the host reduce the margin.
Isacc's goal seemed to spark a revival as the men in Blue spurred by the crowd put everything into the game.
The ATK defence, however, held firm under immense pressure to help gain three points, making it two wins over the Chennai team for the season.
This is the seventh loss for Chennaiyin from 10 matches.
The third and decisive goal came following a melee near the CFC goal.
Lanzarote swung a corner in from the right and John Johnson at the far post attacked the ball and headed it towards the goal.
Carlos Salom was in the right position and blocked it.
In the chaos, he caught the ball, thinking a foul would be given.
But the referee pointed to the spot and signaled a penalty.
Renthlei and Salom argued with the referee over the decision and received yellow cards in the process.
The skipper scored from the spot as he did earlier, sending Sanjiban the wrong way, to tighten ATKs grip on the game before CFCs late assault.
The first half was an entertaining one with the two teams enjoyed a lot of opportunities and there were missed chances too.
Though Chennaiyin enjoyed greater possession, ATK always looked threatening when moves were initiated from the right wing.
In the sixth minute, ATK had a chance.
His shot was saved by Sanjiban Ghosh, who punched it away.
In the very next minute, Isaac played Raphael Augusto through on the left wing and he makes his way inside the box.
Hs hit a low ball across the face of goal and found Andrea Orlandi, who shot first time with his left but it went wide of the post.
ATK's first goal game in the 14th minute when Jayesh Rane smacked one into the top left corner from some 30 yards leaving Sanjiban Ghosh no chance.
The home side found the equalizer in the 24th minute when Thoi Singh latched on to a pass from Mailson Alves and drilled a shot past the ATK custodian.
The goal came on the back of some good moves by the Chennaiyin team, who appeared to get better with every passing minute.
The penalty came when Lanzarote's shot from a Hitesh Sharma pass hit Eli Sabia's hands and the referee pointed to the spot.
The two teams started off brightly, looking to go on the attack from the word go.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)