The win gave three crucial points to Bengaluru FC, who are now leading the points table wih 18 points from six wins in nine matches.
Chennaiyin FC and FC Pune City are placed at second and third places respectively with 17 an 16 points.
The lone goal came in 39th minute as Chhetri latched on to a gift by Conor Thomas in midfield before unleashing a terrific shot.
Bengaluru FC could have scored their first goal in 38th minute but Rahul Bheke failed to tap the ball in the rebound after Edu Garcia's free-kick met Paartalu's head inside the box which struck the far post.
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ATK yet again survived Bengaluru onslaught in 82nd minute as Paartalu picked Garcia's run into the box with a lovely lob. Garcia's shot at the post was saved.
Bengaluru were the better side in the first half, but ATK had their chances.
The biggest chance for the visitors came in 26th minute but Rupert's shot was blocked by Gurpreet Singh.
Gurpreet once again came to his side's rescue in 59th minute by pulling off a good low save after Keane created space and shot at the post.