Desai hit 13 fours in his 137-ball innings and shared 149 runs for the fifth wicket with Darshan Misal (69) from 25.2 overs as Goa chased down the target of 284 with five balls to spare at the NSC Ground here.
Desai's match-winning knock overshadowed Kerala medium pacer Basil Thampi's fine six-wicket haul for 51 runs as Goa lower oder batsmen managed to hold on their nerves in the final overs to reach 287 for eight and win the match.
Chasing the stiff target of 284, Goa were in trouble early on as they were reduced to 36 for three in the sixth over and then slumped to 64 for four in the 13th over before Desai and Misal's rescue act.
Desai was the sixth man out in the 45th over with Goa needing another 31 runs with four wickets in hand. But, they lost two quick wickets and were reduced to 266 for eight in the 47th over.
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Brief Scores:
Kerala: 283 for 7 in 50 overs (Sachin Baby 100, Amit Verma 56; Harshad Gadekar 5/74).
Goa: 287 for 8 in 49.1 overs (Amogh Desai 124, Darshan Misal 69; Basil Thampi 6/51).