The 26-year-old -- who ended last year's competition as runner up to Nick Kyrgios -- proved too strong for the unseeded Frenchman as he powered to a 6-3, 7-5 win.
Despite suffering a scare in the second set when Mannarino -- fresh from his semifinal win over top seed Marin Cilic -- found himself a break up, the No. 4 seed recovered to claim both the set and his fourth career title.
The Belgian -- who had gone three years without claiming an ATP crown -- has now won two tournaments on the bounce, adding to the title he picked up at last week's Shenzhen Open.
"It's a really special trophy for me, as I won the tournament last week and now have again today," Goffin told atpworldtour.com after the match. "It's a special feeling at a tournament I like. I have a lot of happy memories in Tokyo. It's difficult to describe my feelings."
In addition to adding to his accolades, Goffin's successes in the Far East have brought him closer to booking a place at next month's ATP World Tour finals.
After starting the week in 13th place in the Race To London, the World No. 11's latest victory in Tokyo propels him to eighth, one spot higher than Spain's Pablo Carreno Busta.
The in form Goffin -- now unbeaten in his last nine matches -- will be hoping for further success as he returns to China for next week's Shanghai Masters.
"It's important for me to stay fresh physically and mentally with potentially the [Nitto] ATP Finals ahead and then playing for Belgium in the Davis Cup final," the Belgian added.
"I am ready to fight and I want to keep winning."