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The hosts lead 1-0 thanks to a 59th minute freekick goal from Ajaraie that rolled in from the clutches of the Blasters goalkeeper.
Apart from Thrissur's Jithin, NorthEast United's main squad features two other Keralites.
Kerala Blasters' latest signing Noah Sadaoui takes the Golden Boot.
Alaeddine Ajaraie scored in 3-0 win for NorthEast United in the semifinals.
Shillong Lajong defeated East Bengal 2-1 in a quarterfinal.
The Highlanders, who were last in the table in 2022-23, finished seventh with 26 points from 22 matches.
Chennaiyin FC are peaking at the right time and they now stand at 27 points from 21 matches.
Nestor Albiach handed the Highlanders a deserving lead in the 84th minute. Keralite Jithin M S doubled the lead in injury time.
Mumbai City won 4-1 to take their points tally to 39.
Wilmar Jordan Gil scored in the 63rd minute in a 1-0 win for Punjab.
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