Marco Materazzi's men entered the last four with high hopes after finishing top in the regular season.
However, their hopes of making the final hang by a thread as they were beaten 3-0 in Saturday's first leg in New Delhi.
A quickfire first-half double from Ishfaq Ahmed and Iain Hume put Kerala in control, before Sushanth Mathew's 90th-minute goal put David James' side on the brink of the final.
Despite the daunting task Chennaiyin face, Materazzi insists all hope is not lost in Tuesday's second leg in Chennai.
Speaking in the aftermath of the first leg, the Italian said: "It is a very good result for Kerala and we have a lot to do in the second leg, especially because the third goal in the end makes it even more difficult for us.
"But it is important to believe in ourselves and try to fight back on Tuesday."
One crumb of comfort for Chennaiyin is that they defeated Kerala twice in the regular season.
But Kerala's home defeat to Chennaiyin is the only time they have been beaten on their own turf this season.
The other semi-final is much more finely poised with Atletico de Kolkata and Goa having played out a 0-0 draw in Sunday's clash at the Salt Lake Stadium.
Zico's Goa, who have a fitness doubt over left-back Narayan Das, have yet to beat Kolkata in the ISL.
However, Goa can take confidence from Atletico's poor run of form that has seen them fail to win their last six matches.
And Brazil legend Zico remains confident that his team can get the job done in Goa.
"As I have said before, it is a game of 180 minutes," he said.
"The first 90 minutes are over and now we have to see how the next 90 minutes go. I am 100 per cent confident and I hope that we win the next match."
