Chennaiyin finished top of the regular season standings, beating Blasters in each of their two meetings.
But that counted for little in their first-leg meeting in New Delhi on Saturday as first-half goals from Ishfaq Ahmed and Iain Hume put David James' side in control before a stunning 90th-minute curler from Sushanth Mathew.
This gives Marco Materazzi's men a mountain to climb if they are to overturn a three-goal deficit in Tuesday's second leg and reach the showpiece final.
"Nothing is impossible in football, but it will be important not to concede in Chennai," Materazzi told the league's official website.
"The first half will be very important and we will have to take our chances."
The chances of reaching the final appear far more favourable for both Atletico de Kolkata and Goa, after the pair played out a goalless draw in their semi-final first leg on Sunday.
Goa finished second in the regular season standings, ahead of Kolkata in third, but took just a single point from their two meetings.
Zico's side had the better of the first leg away from home, however, registering 10 shots on target to Kolkata's one.
But Antonio Lopez Habas' men clung on for a 0-0 draw that gives them every chance of advancing, heading into Wednesday's return leg.
