The No. 21 seed continued his strong season after returning from a wrist injury that forced him to miss the U.S. Open past year and will play either No. 6 seed Novak Djokovic or unseeded John Millman on Friday.
The match was a repeat of the 2014 US Open final, which Cilic won, and the Croatian made a strong start as he took the opening set.
He lifted the trophy in 2011 and 2015.
Yet there was a dramatic and somewhat unexpected shift in momentum as Nishikori reeled off four games in a row to level the match before also claiming an early break in set three, maintaining a ideal record of taking every chance he was getting on the Cilic serve. Millman also went up 1-0 in the final set, before Djokovic earned a 3-1 edge.
"Very tested", said Djokovic, who admitted that like many he was surprised to find himself facing Millman, not Federer, across the net.
She pushed some balls a few feet past the baseline, often failing to make Osaka do anything special to win a point and finishing with 31 unforced errors. Djokovic looked exhausted after a 60-minute first set, but was given a brief break as Millman requested a change of clothes due to the extreme humidity. "I was not feeling well", she said.
"I needed that rest", said Djokovic, who finally gained the decisive break in the penultimate game of the final set then served it out at love. "I think it would be really cool".
"I definitely left it all out there today and pulled up a bit short". "I think she can win a title now, even though grand slam".
In the match before Nishikori's, Naomi Osaka moved into her first Grand Slam semifinal by routing Lesia Tsurenko 6-1, 6-1 on Wednesday in the U.S. Open quarterfinals.
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Nishikori stunned then-world number one Djokovic in the semi-finals in 2014 to become the first man from an Asian country to reach the championship match of a major.
"Yeah, it's great news we're both in the semis".
Cilic did level at 4-4 but his erratic play continued as Nishikori stole the set with the help of two double faults in the tiebreak.
"It's great to see", said Nishikori.
Having recovered from 3-1 down to lead 4-3 in the breaker, Cilic double-faulted twice in succession and another missed first serve proved costly at set point down as Nishikori pounced on the second delivery with a backhand return victor.
Millman fought back to take a 4-3 lead before Djokovic finished him off by winning the final two points of the game.
The tide continued to turn in the third as Nishikori chipped away at the faltering Cilic with a third successive break.
"I tried to fight on every point, even though I was really exhausted", Nishikori said.
"Especially in the end I really focus on every point", he said but added: "I wish I don't go to five sets every time".