The Tuskers now have 16 points from seven matches, three clear of FC Goa who have played two matches less.
Chennaiyin FC beat Tribhuvan Army 3-0 to enter quarter-finals
Chennaiyin FC beat Delhi FC 2-1; Gokulam qualifies following Bengaluru-Blasters draw
Brandon Fernandes returned to the side as Goa coach Juan Ferrando named three changes to the line-up that lost against ATK Mohun Bagan with Aiban Dohling and Jeorge Ortiz being the other two.
On a night of missed opportunities, the two-time champions rode on goals from Rafael Crivellaro and Nerijus Valskis in the 57th and 59th minutes respectively to pocket three points, which takes it to sixth in the points table with 15 points.
India international Anirudh Thapa scored in the first minute to set up Chennaiyin FC's 2-1 win over Jamshedpur FC in an Indian Super League match, in Vasco, on Tuesday.
Adam Le Fondre smashed in a 75th-minute winner after Hernan Santana (45th) had cancelled Jakub Sylvestr's first goal.
A 56th-minute penalty strike from Sunil Chhetri was the difference between the two teams
It was a second successive draw by the Csaba Laszlo-led side as they once again squandered plenty of chances to settle in the seventh place with 10 points from eight matches.
Two-time champion Chennaiyin FC opened its account in ISL-6 with a goalless draw against Mumbai City FC in its first home game of the season at the Nehru stadium, in Chennai, on Sunday.
It was Chennaiyin FC's first win in 289 days, bringing a lot of relief for Gregory, who two weeks ago was contemplating an exit.
Goian's 83rd-minute strike was enough for Chennaiyin to win the contest 1-0 and complete the ISL play-off lineup.
ATK may have qualified for the play-offs, but the loss came as a big blow to their AFC Champions League qualifying aspirations with FC Goa taking a three-point lead at the top with only a match left for the league stage to conclude.
A rampaging ATK claimed an unprecedented third Indian Super League title triumph with a 3-1 victory over arch-rival Chennaiyin FC in a summit showdown that was played behind closed doors in Margao on Saturday. Javier Hernandez (10th minute) and Edu Garcia (48th) put ATK in the driving seat but Nerijus Valskis (69th) reduced their advantage to set up a tense end to the contest. Hernandez scored another in injury time (90+4th) to confirm a record third title.
Chennaiyin FC went through to the final 6-5 on aggregate, thanks to their 4-1 victory at home in the first leg.
Real Kashmir scored their first victory of the ongoing I League season with a 2-1 defeat of the defending champion Chennai City.