If Chennaiyin beat Manang and Minerva either win or hold Abahani, the Chennai-based side will go through to the knockout phase of the tournament.
The 26-year-old from Neyveli will be moving to Chennaiyin FC after three seasons at Chennai City FC, with whom he won the 2018-19 I-League title recently.
With Wednesday's result, Abahani drew level with Chennaiyin on top of group on seven points from four games.
The club announced on Saturday that the Englishman had agreed to a one-year extension to his deal.
The late winner itself may have been rather fortuitous, but Chennaiyin coach John Gregory won’t care.
The visiting Bangladeshi side made a bright start and Kervens Belfort flashed a header wide from Rubel Miya's corner in the second minute.
There is another curious link between the two teams. Chennaiyin’s assistant coach Syed Sabir Pasha turned out for Dhaka for two seasons in 1999 and 2000.
CFC had defeated Nepal's Manang Marshyangdi Club 2-0 in their previous outing before playing out a goalless draw with Indian rivals Minerva FC in their opening match.
It took three minutes for Chennaiyin FC to inject some life into their AFC campaign.
What a difference a couple of weeks can make! When Chennaiyin FC last trotted out at The Arena, they were clutching at straws.
Chennaiyin won the 2017-18 Indian Super League but had a disastrous outing in the just-concluded season as they finished at the bottom of the table.
Brandon Fernandes scored a goal befitting of a title winner in the 64th minute to seal the contest in Goa's favour.
Winning the Super Cup will help Sergio Lobera's side soften the blow and claim silverware for the first time in the club's history.
The former Indian Super League (ISL) winners will meet FC Goa in the title clash at the Kalinga Stadium on Saturday.
Mailson Alves equalised in the 33rd minute before Anirudh Thapa made it 2-1 for Chennaiyin with a brilliant solo goal in the 40th minute.