Top seed Stan Wawrinka overpowered American qualifier Austin Krajicek 6-3, 6-4 to join him in the last four, though the Swiss required less than an hour to take care of business on a sunny afternoon in Tokyo.
Second seed Nishikori was greeted like a rock star by 12,000 screaming fans but Cilic, who beat Japan's golden boy in last year's US Open final, had failed to read the script and quickly seized the initiative with some thunderous hitting.
Serving with such ferocity he knocked the racquet out of Nishikori's hand, the sixth seed broke first with a thumping forehand drive to lead 4-2 before wrapping up the opening set with an ace down the centre.
Nishikori is a tough nut to crack on the Tokyo hardcourts, however, having captured the Japan Open twice in the last three years.
And when cracks began to appear in Cilic's armour, he levelled with an acrobatic leaping backhand that the lanky Croat could only dump into the net.
Cilic's game unravelled under the onslaught in the decider as Nishikori caught fire, breaking for 3-1 and closing out the quarter-final with an ace after two hours, 11 minutes to ensure 'Nishikori Fever' stretches into the weekend.
"When I drove past all the fans on the buggy after practice this morning, I thought: 'This is what it must feel like to be a lion in a zoo'," joked Nishikori, who is regularly mobbed on his return to Japan.
"The wind made it difficult today but I hung in and waited for my chances," added the Japanese superstar. "I had a couple of dangerous moments out there but that happens."
Nishikori, bidding to win a fourth title of the year, next faces Benoit Paire -- the man who stunned him in the first round of this year's US Open -- after the Frenchman beat volatile Australian Nick Kyrgios 3-6, 6-4, 6-1.
World number four Wawrinka's path to the final was made easier when third seed Gilles Simon of France crashed out 6-3, 6-4 to Luxembourg's Gilles Muller.
Wawrinka made no mistakes as he powered past Krajicek in just 58 minutes, and the left-hander had no answer to the rapier-like ground strokes of the French Open champion.
Wawrinka's one-handed backhand -- one of the most venomous shots in men's tennis -- did much of the damage and he closed out the match with a kicking serve which a deflated Krajicek swatted wide and long.
"I felt a bit more relaxed today and confident with my game," said Wawrinka, who is chasing a fourth title of the year and the 11th of his career.
"A one-hour match, it was the perfect day for me today."
Source: AFP
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