Both received walkovers when their semifinal opponents withdrew for health reasons. That left Nadal and Djokovic to play for the title Sunday in their 40th career meeting and their first of 2014.
The wave of ailments left the tournament with only two women's doubles matches for disappointed spectators. Former No. 1 Martina Hingis advanced to her first doubles final since 2007 when she and Sabine Lisicki beat Cara Black and Sania Mirza 6-3, 6-4.
On Saturday, No. 1 Serena Williams will try for her seventh Key Biscayne title when she plays No. 2 Li Na — health permitting.
Djokovic also received a walkover in the third round and has played only six sets in the tournament. He's seeking his fourth title in the event, while Nadal is 0-3 in Key Biscayne finals, one of only three ATP Masters 1000 tournaments he has yet to win.
Djokovic will try to complete a March sweep Sunday. He won the Indian Wells title two weeks ago, when he beat Federer in the final.
Nadal leads his rivalry with Djokovic, 22-17, and they went 3-3 last year. Regardless of Sunday's outcome, Nadal will remain No. 1 and Djokovic No. 2 next week.
A disappointed Nishikori pulled out less than two hours before his semifinal.
“I tried to warm up and I couldn't move” Nishikori said. “With anybody on the other side, I don't think I could win today.”
Berdych's withdrawal was announced an hour before his match. That spared him from having to face a player who has won their past 16 meetings.
Nishikori said his groin has bothered him for more than a month, and he retired during a match in Delray Beach last month. This week he won a won a three-set match against David Ferrer, saving four match points, and then beat Roger Federer in a three-setter Wednesday night.
The No. 21-ranked Nishikori said he won't need surgery, but he's unsure how long he'll be sidelined and will fly home to Japan to see a doctor. His next scheduled match is in Davis Cup for Japan against the Czech Republic in Toyko on April 4.
Nishikori has retired or withdrawn 14 times in his career, including three times in Grand Slam events. He was hoping to reach his first ATP Masters 1000 final.
“It was going to be a great challenge for me today,” Nishikori said. “Hopefully I can play another time.”
Three of the past six Key Biscayne men's semifinals have been canceled. Nadal withdrew because of a knee injury in 2012, giving Andy Murray a walkover.
Spectators on Friday will be offered a chance to exchange their tickets for a session at the 2015 tournament.