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Asif headed home the winner in the first minute of added time to earn Kerala three points.
Viknesh has been replaced in the 22-member squad by reserve player Asif O M from Ernakulam.
Goalkeeper Midhun V will lead the 22-member squad.
Kasaragod-native VP Muhammad Ali watched his son make his Kerala debut and score just a two week ago.
Defending champion Kerala topped the group with 15 points from five matches.
The defending champions moved to the top of the Group II table with a maximum 12 points from four games, ahead of Mizoram on goal difference
Mizoram lead Group II with 12 points from four matches followed by Kerala who have nine from three games.
Mizoram edged out Jammu and Kashmir 3-2 in the first match of the day.
Holders Kerala swamped Rajasthan 7-0 in their opening match of the Santosh Trophy National Football Championship.
The squad features 16 new faces. P B Ramesh has been named the coach.
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