Nandhakumar Sekar goal clinched a 3-2 win for the Juggernauts after Chennaiyin FC had scored the equaliser in the 94th minute via an Abdenasser El Khayati penalty.
Thomas Brdaric was disappointed with his side's performance during the opening exchanges but praised his team's fighting spirit despite being put under pressure on several occasions during the game.
Roy Krishna scored inside five minutes to give the Blues an early advantage but Prasanth Karuthadathkuni scored at the stroke of half-time to restore parity.
Chennaiyin, making a much-awaited return to the city, will come into the match in high spirits after kickstarting their campaign in style, beating ATK Mohun Bagan 2-1 in the opening fixture earlier this week.
Speaking to the media ahead of the team's opening fixture, head coach Thomas Brdaric said that his side will be seen playing an attractive brand of football.
As part of the preparations for the season, Chennaiyin FC will take on fellow ISL outfit Odisha FC in a friendly encounter on Saturday at the SRMC Ground in Chennai.
Both sides shared a similar fate in the group stage as the Islanders collected seven points from four games and topped their group while the Marina Machans picked up as many points and finished second in their group.
Chennaiyin FC beat I-League sides TRAU FC and NEROCA FC 4-1 and 2-0 respectively to finish second in Group C after a poor start and qualify for quarter-finals