The third-seeded Federer, playing in front of his home country crowd, bested Nishikori 6-1, 6-3 in only 73 minutes, winning 85 percent of his service points while firing five aces.
The Swiss great, who won the Basel event for the fifth time in the last six years, took advantage of Nishikori's misfiring serve.
The Japanese upset world No. 1 Novak Djokovic in Saturday's semifinals but couldn't continue the momentum Sunday.
Nishikori put his first serve in play only 46 percent of the time and recorded four double-faults.
2014: NFL Cheerleaders [PHOTOS]
Michael Sam cut from the Dallas Cowboys