Both advanced when their semifinal opponents withdrew for health reasons. They'll play for the title Sunday in their 40th career meeting and their first of 2014.
Djokovic received a walkover for the second time in the tournament when Kei Nishikori withdrew because of a left groin injury. Four hours later, Tomas Berdych withdrew before his match against Nadal because of gastroenteritis.
The No. 2-ranked Djokovic will be bidding for his fourth Key Biscayne title. Regardless of the result, Nadal will remain No. 1 next week.
Nishikori won a grueling three-set match against Roger Federer on Wednesday night and also won a three-setter against David Ferrer in the fourth round, when he saved four match points.
Nishikori tweeted the news after he tried to practice before the match.
"Very disappointed and I am obviously very sorry for any fans," he said.
The two cancelled matches left the tournament with only two women's doubles matches.
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.