Raphael Augusto put the visitors ahead in the 27th minute before Atletico produced the turnaround with a superb display by man-of-the-match Sameehg Doutie.
The South African right winger brought in the equaliser before the interval and produced a fine assist in the 63rd minute for Iain Hume to score his fifth goal in the tournament.
Atletico jumped to the second place behind leaders FC Goa with 17 points from 11 matches, while Chennayin were rooted to the bottom of the table with 10 points from as many matches.
Raphael Augusto put Chennayin ahead in the 27th minute when the Brazilian took advantage of some sloppy defending by Augustin Fernandes to make a clincial finish.
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Augusto played a little one-two with Fikru and made his way into the box after the Atletico left back made a failed diving attempt to clear the ball.
Arnab Mondal too came in his way but once Augusto went past Fernandes there was no stopping him as the Brazilian calmly slotted the ball home.