In a match between last year's finalists, both the teams had their share of chances but it was ATK's Ryan Taylor who did the star act by scoring one and setting up another for a hard-fought draw.
Under Sheringham, the defending champions suffered four losses and drew thrice in 10 outings to slip to eighth place in the 10-team standings.
Pune City had registered a convincing 1-4 victory against the defending champions in Kolkata and many believed ATK would seek their revenge.
Zequinha was the star of the show, striking in the 73rd minute to give his side the lead and the winner.
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.
The former Ireland and Spurs player injected life into the game with a spectacular finish in the 78th minute to score his first goal of the season.
The victory also lifted ATK from the bottom of the table to the eighth spot with five points to their credit.
Mumbai City FC coach Alexandre Guimaraes admitted that ATK were a tough side as their playing style was different.
Ryan, a versatile player and former England under-21 international, has the ability to play as a full-back or across the midfield.
Chennaiyin coach John Gregory has used the same winning combination for the last two matches but may be forced into making a couple of changes to tackle the visitors.
Last season's Golden Boot winner Marcelinho once again proved why he was the biggest threat as he struck a double and assisted two goals for Pune.
ATK were held to a goalless draw by Kerala Blasters in the ISL opener in Kochi as they are missing their star Tottenham Hotspur recruit Robbie Keane.
This was the first time that ATK drew their first away match in an ISL edition, having won in the earlier three occasions.
Defending champions ATK play Kerala Blasters in Kochi in the opening match of the fourth season.
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