Federer, playing in his 98th ATP final of which he has won 68, triumphed 6-1, 6-3 against the 21-year-old Japanese wild card, who was playing in his third.
"He didn't give me a chance, he was too good for me today," said Nishikori, who beat world number one Novak Djokovic in the Basel semi-final.
Federer, who completed his third match without dropping a set following his wins against Andy Roddick and Stanislas Wawrinka, won his second title of the year and his first since Doha in January.
Nishikori, meeting his idol Federer for the first time, held his serve in the opening game but the dominant Swiss rattled off the next seven as he totally dominated proceedings against the world number 32.
The Swiss, playing in his first tournament since the US Open in September, hit five aces and no double faults while Nishikori took only six points off Federer's serve.
Nishikori put up more resistance in the second set, saving two break points in the second game to at least end Federer's run.
However, it was only a matter of time and Federer broke in the sixth game. Nishikori defiantly saved four break points but could do nothing about a perfect Federer lob which left him stranded on the fifth.
The Japanese had his only break point in the ninth game but Federer saved it and went on to finish off the match with a forehand smash.
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Source: bdnews24.com
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