Rana Gharami tested positive for a banned substance in a first such case involving an Indian Super League footballer.
A late winner from Ankit Mukherjee (88th) clinched three points for ATK.
Both ATK and Delhi Dynamos have failed to qualify for the Indian Super League (ISL) play-offs for a second successive season.
A fairly one-sided affair saw Gianni Zuiverloon scoring a fantastic goal while Rene Mihelic netted one from the spot.
Daniel Lahlimpuia, Bikramjit Singh and Nandhakumar Sekar scored in Delhi's memorable win in Chennai.
Jamshedpur completed the comeback after the break with a 61st minute match-winner from Farukh Choudhary.
Mumbai City FC climbed to the fourth spot in the table, while Delhi Dynamos are rooted to the bottom without a win to their name.
Delhi Dynamos, who are rock bottom of ISL 2018, host fifth-placed Mumbai City FC at the Jawaharlal Nehru Stadium on Monday.
Udanta Singh notched the winner for Bengaluru FC in captain Sunil Chhetri's 150th game.
FC Goa came from behind with two late goals in a gap of eight minutes to edge past Delhi Dynamos 3-2.
Delhi Dynamos were denied their first win of the Indian Super League 2018 as Tiri scored the equaliser for Jamshedpur FC in the 77th minute of the game.
The win over Delhi Dynamos gave NorthEast United their third win in five matches this Indian Super League (ISL) season.
The three points took Mumbai to the fifth spot on the table while Delhi remain at the eighth position.
Andrea Orlandi could have opened the scoring for Chennaiyin FC in the second minute of the match.
Noussair El Maimouni scored the winner for ATK in the 84th minute.
Rana Gharami became the first Indian footballer to score the goal in ISL 2018-19 season.
Miguel Angel Portugal had left Delhi Dynamos and was then roped in by FC Pune City.
Pune City lost 0-4 against Goa in their penultimate clash but their impressive performances earlier in the season means they don't have to wait for the final league clash to secure a point for a place in the play-offs.