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Spanish forward Sergio Mendigutxia scored the winner for the defending champions in the 80th minute.
The 29-year-old Bonet took Rajasthan United to sixth place in their debut season in the I-League.
The Malabarians made public the news through their official Instagram handle, in which it thanked Towa for his time with the team.
Gokulam remain in third place with 15 points from eight matches.
Everton Kaka, 31, has played for clubs in Brazil, Portugal and Saudi Arabia.
The 52-year-old replaces Italian Vincenzo Albreto Annese.
Vincenzo Alberto Annese won back-to-back I-League titles besides the prestigious Durand Cup for the Kozhikode-based club.
In the final matchday, Gokulam Kerala came from behind to defeat Sethu FC 3-1.
Vincenzo Alberto Annese made a strong case for India's second-tier men's competition, I-League with a thumping victory over ATK Mohun Bagan.
The I-League champions ran out 4-2 winners in the clash to two Indian heavyweight clubs in Kolkata.
Results 51-60 of 93
