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FC Goa beat ATK Mohun Bagan 1-0 in the final Group C match.
Jamshedpur won 3-0 to finish top of Group C and enter the semifinals.
Liston Colaco scored a brace for the winners, while Hugo Boumous, Manvir Singh and Kiyan Nassiri also found the mark for the ISL champions.
Kerala Blasters fans were quick to remind Parth Jindal of controversial officiating when their teams clashed in the knockout.
After a thrilling 2-2 at the end of extra time, ATK MB prevailed 4-3 in penalty shootout.
The title clash between ATK MB and Bengaluru FC will be played in Goa on Saturday.
The second leg of the semifinal contest will be held at Kolkata on Monday.
ATK MB won 2-0 with Boumous and Petratos scoring in Kolkata.
Kerala Blasters lost 1-2 after scoring first in Kolkata.
Bartholomew Ogbeche came on as a substitute and scored the only goal of the match in the 86th minute as the Mariners went three successive games without a win for the first time this season.
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