Fish had been trying to reach the semifinals for the fourth time in his last five tournaments, but he fell 6-3, 6-2.
Nishikori will take on Pablo Cuevas in the semifinals after Cuevas outlasted Guillermo Garcia-Lopez 1-6, 7-6 (7-4), 6-3.
The other semifinal will send Ivo Karlovic against Ryan Sweeting.
Karlovic defeated John Isner in 3-hour match 7-6 (7-2), 6-7 (2-7), 7-6 (11-9). Sweeting, who will play in his first semifinal match on the ATP tour, eliminated Teymuraz Gabashvili 3-6, 6-3, 6-1.