"We have never met in a Grand Slam final, I have great respect for him as a person and a player, he is a great guy," said Djokovic, who missed the 2017 tournament due to injury.
"He has had many injury problems in the past, but he is a great player."
Wimbledon champion Djokovic, playing in his eleventh US Open semifinal, claimed the 15th victory in 17 games against Nishikori.
It was easy for the 31-year-old Serbian who is pursuing a 14th Slam title to put him at the level of Pete Sampras on the all-time list.
He broke the service four times, while Nishikori, who was below his level, saved 13 of the 17 break points he faced and committed 51 unforced errors.
Nishikori runs out of gas
Nishikori stumbled on a circular saw in the shape of Djokovic on Friday, but the Japanese star leaves the US Open satisfied with a semifinal race one year after missing the tournament due to injury.
"It was very good," he said of his two weeks at Flushing Meadows. "Maybe not today, but in the last few matches I played great tennis, I beat a couple of good guys.
"I'm really happy to be in the semifinals again, I could have been better at playing the final again, but maybe it's my next opportunity."
Nishikori made history by reaching the final of the 2014 US Open, but said he could hardly be forced to watch the tournament last year while battling a wrist injury that led to his 2017 season to a premature close.
Little by little he started making his way in 2018, gaining confidence gradually with a quarter-final race at Wimbledon and his appearance in the last four here.
He dug deep for a five-set victory over Marin's seventh seed, Cilic, in the quarterfinals, and may still have felt the effects against Djokovic.
"I think he was tired of the last games," he said after his 6-3, 6-4, 6-2 loss to Djokovic.
"I tried to give 100 percent, but he was playing very solid.
"Maybe if he was not Novak, he could have had a chance, but he was playing great tennis today, serving, coming back, hitting the floor, playing aggressive and not having much energy to be with him."