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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.
The visitors took 26 shots but failed to get a goal in Jamshedpur on Thursday.
Javi Hernandez and Roy Krishna scored in the 2-1 win for Bengaluru.
However, the Mariners could drop to fourth if Kerala Blasters win their game against NorthEast United FC on Sunday. Odisha FC dropped out of the playoff spots and are now seventh.