Desai triumphed 11-3 6-11 11-6 11-9 5-11 11-6.
Earlier, the fourth seed had beaten compatriot Soumyajit Ghosh 10-12 11-8 6-11 11-1 11-4 11-4 in the semi-final to earn a meeting with Nuytin.
Desai said that he needed to win the title after a long drought.
"This title win has come after a long time and I needed to win this," said Desai from Santos.
The title clash turned out to be a riveting one after both the finalists had caused upsets in the earlier rounds.
Desai took the first game rather easily while losing the second. The Indian took the next two games but let his opponent, who took an early lead, built on it to lose badly.
However, Desai was up to the task in the decider and clinched the title with three straight points.
"I haven't won a title for nearly a year. Cedric was good with his game, often surprising with some great attacks. In the decider I kept my cool and return whatever he sent from across the table and it helped me win the title," said Desai.