Klizan had won their only previous match at last year's French Open, but Nishikori dominated their second meeting on the same outdoor court where he won his first clay-court title.
Nishikori won the first five games of the match and saved all six of Klizan's break points.
The 25-year-old Nishikori is trying to add to his eight career titles.
"I am really excited to come into the final again here," Nishikori said. "I played a really solid match today, everything was perfect. I am very happy with the win and the way I am playing."
Nishikori had another strong start by claiming 21 of the first 27 points with a complete mix of winning shots, including a beautiful lob that fell on the line.
Nishikori closed out the first set with a slicing backhand approach shot and broke Klizan for the second time in the second set to close out the win in 1 hour, 17 minutes.