Fifth seed Nishikori reached the final here last year but will lose a chunk of ranking points after he hit 25 unforced errors and just 14 winners in succumbing to Frenchman Herbert.
"I'm very happy to finally beat Kei," the 49th-ranked Herbert said. "I was very confident with my defence.
"I came to the match with good feelings after the first round." Nishikori lost the Monte Carlo final a year ago to 11-time champion Rafael Nadal.
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