After Naomi Osaka had routed Ukraine's Lesia Tsurenko 6-1 6-1 to become the first Japanese woman in 22 years to reach a Grand Slam semi-final, Nishikori followed his compatriot into the last four in a match lasting over four hours.
It was a much different outcome from four years earlier when the big-hitting Cilic floored the Japanese counter-puncher 6-3 6-3 6-3 to claim the U.S. title.
Cilic has made two Grand Slam finals since but Nishikori has never been back and will now take on either twice U.S. Open champion Novak Djokovic or unseeded Australian John Millman for a spot in Sunday's final.
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Initially, it looked like the match might follow a similar storyline from 2014 when seventh seeded Cilic took the opening set from a sluggish Nishikori.
The Japanese sputtered along until earning his first break chance at 2-4 in the second set and was able to convert to get back on serve.
As Nishikori began to find his rhythm Cilic suddenly started to misfire, the Japanese 21st seed collecting a second consecutive break on a double fault to surge in front 5-4 before holding serve to level the match.
The tide continued to turn in the third as Nishikori chipped away at the faltering Cilic with a third straight break.
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.
The Croat rebounded to take the fourth and the rollercoaster ride continued into the fifth with Nishikori grabbing the advantage with a break at 3-1 and taking Cilic's serve again with a blistering return winner to close out victory.
(Editing by Ed Osmond)
