The 26-year-old was dominant from the start and broke Mannarino to take a 3-1 lead in the opener and maintained the one-break advantage to claim the set, winning 21 of 25 points on his own serve.
World number 31 Mannarino rallied in the second and broke Goffin to take a 4-2 lead but the in-form Belgian responded by breaking the Frenchman immediately and once more in the 11th game as he charged to victory.
The win in Tokyo was Goffin's fourth career title and second of the season after his ATP 250 Shenzhen Open triumph last Sunday.
The world number 11 will next travel to China to play in the Shanghai Masters.
(Reporting by Aditi Prakash in Bengaluru)
