Nishikori's fourth-round win over fifth seed Milos Raonic matched the record for the latest finish at Flushing Meadows with two other matches at 02:26 local time (06:26 GMT).
When Wawrinka claimed the fourth set in a tie-break at Arthur Ashe Stadium on Wednesday, most would have written off chances of Nishikori going the distance - with the Swiss having a fitness edge after receiving a walkover in the third round.
But Nishikori defied the doubters to win the fifth set 6-4, and progress to his maiden major semi-final.
Wawrinka said he never thought Nishikori would be flat as the match wore on.
"From outside he looks really dead, but we know on the court he can play, and he play long like what he did today," Wawrinka said.
"If even at the beginning he looks like he's going to die on the court, but he's there. Physically he's there. Even at the end of the match.
"We were both quite tired in the fifth set. I try not to show [it]. I still think that I was the fresher on the court, but he handled [it] well.
"He was really going for his shots in the fifth set. I had some chances to break him.
"Maybe I should go a little bit more, maybe I should try a few different things, but [it] didn't happen that way."
Wawrinka said he altered his strategy on serve, but it came back to bite him as Nishikori got the crucial break in the 10th and final game.
"I realised that I was trying to make him run even more, so I was trying to always open with my first serve, trying to put a lot of first serves, not give him so much time to have second serve to really come in," he said.
"Was just a decision I took to change a little bit. Except the last game I was really in control of my serve on the fourth and fifth set. I had really two bad games on my serve."
The result ended the grand-slam season for Wawrinka, who began it with a stunning title win at the Australian Open that catapulted him into the top echelon.
The Swiss said breaking through at the level had made it no easier for him to contend at grand slams.
"It's a really long way to win a grand slam, even if you're in quarter, even if you're in semi-final," he said.
"It's better not to think too much about that, especially when you see who is still playing in the draw. I was ready for the fight. I was ready to play.
"I'm a little bit disappointed with myself, with the level I had today. I don't think I played a great match.
"I think I was a little bit hesitating with my game. I didn't find a way to take control of the rhythm of the match big time because he was playing well, but I still think that I should maybe try something different."