MORE: Novak Djokovic and Roger Federer will continue their battle to end the year as world number one when they compete in the Paris Masters
The 17-time Grand Slam champion had lost the last two finals of the ATP 500 hard-court event to Argentina's Juan Martin del Potro, who was absent this time around with a persistent wrist injury.
Federer took full advantage of Del Potro's no-show to claim victory in his 11th final at the event in the city of his birth.
Having limped into Sunday's clash with a hard-fought victory over Ivo Karlovic, world number two Federer needed to make a bright start against his Belgian opponent.
And the 33-year-old did just that - breaking Goffin's serve in the opening game to instantly put himself on the front foot.
Federer faced little resistance from Goffin and, after claiming another break of serve, won the set having won three of his four service games to love.
Goffin - contesting his third ATP World Tour final - put up more of a fight at the beginning of the second set, but found himself a break down when Federer moved into a 3-2 lead.
That setback proved to be the beginning of the world number 28's downfall, as Federer won five consecutive games on his way to sealing the title, to the delight of a partizan crowd at St Jakobshalle.
The victory sees Federer - now on a winning streak of 12 matches - move to within 500 points of world number one Novak Djokovic in the ATP Race to London ahead of next week's Paris Masters, where 1,000 points will be up for grabs.