The ATP Tour and Sony Open tournament officials said on their Twitter feeds that seventh-seeded Czech Berdych had withdrawn from his scheduled evening clash with top-seeded Nadal "due to gastroenteritis."
Nishikori had earlier pulled out of his final-four meeting with Djokovic because of a groin injury.
It was a bizarre turn of events that wiped out the day's singles action but nevertheless produced a predictable pair of finalists in the tournament's top two seeds.
Berdych was at a loss to explain how he became so ill.
"Last night was basically the same as every other night. I ended up in the same restaurant, everything was fine," he said in comments the tournament posted on Twitter.
"I woke up at 7:30 in the morning with pain in my stomach. I am disappointed about not getting a chance to play," he added.
Nishikori withdrew after attempting to warm up for his early match against Djokovic, saying the left groin injury hindered his movement too much to allow him to play.
The injury ended Nishikori's sparkling run at the hardcourt tournament -- where he saved four match points en route to a fourth-round victory over world number five David Ferrer and then vanquished Swiss great Roger Federer in the quarter-finals.
"For me it was my biggest tournament in a couple of years, to reach a semi-final of a Masters," a dejected Nishikori said in a hastily convened press conference. "It's really sad. I was really playing well."
Nadal, who has never lifted the Miami trophy, has three runner-up finishes on his resume, including a loss to Djokovic in a third-set tiebreaker in the 2011 title match, one of the three times Djokovic has won this title.
The pair will be meeting for the first time this season.
Nadal leads their career head-to-head 22-17, but Djokovic has won their last two encounters, in the finals in Beijing and at the ATP World Tour Finals.
Djokovic, who beat Federer for the Indian Wells Masters title two weeks ago, is bidding to complete the tough Indian Wells-Miami double for the second time after accomplishing the feat in 2011.
The Serbian received two free passes in his progress to the final. He also advanced to the fourth round on a walkover after third-round opponent Florian Mayer withdrew from their third-round match with a groin injury.
"Well, it's not the first time it happens for me to have the opponent pulling out -- maybe it's the first time I have twice in the same tournament," he said.
"But it is the way it is, and you kind of have to deal with that."
Djokovic said he practiced well on the stadium court on Friday and would just try to keep himself sharp until Sunday's final.
"I'm trying just to keep up whatever I have been doing the last 10 days," he said.
"I have won Indian Wells, which gave me a lot of confidence, played a lot of matches, put in a lot of hours on the practice court, and hopefully it will pay off."