Nishikori's 6-2, 6-2 victory denied Cilic an opportunity to win back-to-back ATP World Tour titles. Cilic claimed his ninth career title two weeks ago in Zagreb, Croatia, and had won nine of 11 matches this year.
Cilic's loss left the tournament without any of its top four seeds in the semifinals. Second-seed Milos Raonic, third-seed John Isner and fourth-seed Sam Querrey were eliminated by the second round.
Nishikori, the fifth seed, reached his second semifinal of the year. He opened the year reaching the same round in Brisbane.