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Blasters received two red cards but held on to Noah Sadaoui's first-half penalty.
Argentina's World Cup winner Messi, 37, plays for MLS side Inter Miami.
Kerala Blasters have come under pressure from fans following a poor start to the season.
The Swede who was sacked in mid-December has made a scathing attack on the Blasters management.
Talented winger Mohammed Aimen last played on November 7 before suffering an injury.
The referee who officiated the semifinal might have unwittingly contributed to Kerala's defeat in the final.
Striker Robi Hansda scored the winner in the second minute of added time.
The bee attack occurred shortly before half-time in Bengaluru.
Muhammad Roshal PP scored a hat-trick as Kerala won 5-1 in the second semifinal.
Kerala edged Jammu & Kashmir 1-0 with Naseeb Rahman scoring the winner in the 72nd minute.
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