Nishikori, seeded eighth, outlasted sixth-seeded Milos Raonic 7-6 (7-5), 3-6, 6-0. Raonic pounded out 14 aces but only one in the decisive third set.
Nishikori dropped just four points on serve in the final set and won 63 percent of the points off Raonic's serve in the set. He finished off three of his six break chances but didn't allow Raonic a break opportunity.
It was the second career ATP title for Nishikori, whose other win was in February 2008. He is 2-2 in tournament title matches. Raonic, who was looking for his third title of 2012, fell to 3-3 in championship matches.
Nishikori collected $308,130 for the title while Raonic took home the runner-up check for $138,920.