"I had to make some changes," Nishikori said. "He was playing very well at the start. I raised my game in the second set."
Nishikori will meet American John Isner, who survived a tough challenge from compatriot Steve Johnson in the second semi-final.
Isner defeated the unseeded Johnson 6-3 3-6 7-6 (11-9).
In the third-set tie-break, Isner faced match point at 4-6, but managed to storm back for his eighth consecutive match win and back-to-back finals after his win in Atlanta last weekend.
The 25-year-old Nishikori will be chasing his third win of the year and is already assured of moving up a notch to fourth in the world rankings.
Nishikori fell behind 3-0 in the opening set and could not recover, but rebounded with a dominant second set to level the match against the eighth-ranked Cilic.
In the final set, Nishikori led 3-1 and 4-2 lead but Cilic battled back to draw level at 4-4 before the Japanese won the final two games to beat the Croatian in their first meeting since the Open final.
Nishikori, who has now beaten Cilic in six of their nine head-to-head matches, improved his match record this year to 42-9. Only Novak Djokovic (48-3) and Andy Murray (48-8) have more wins on the 2015 ATP World Tour.
(Reporting by Tim Wharnsby in Toronto; Editing by Larry Fine/Greg Stutchbury)
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