
Djokovic, who beat an ailing Federer in an Australian Open semi-final three months ago, became the third opponent from four events to fall at the feet of the world number one, either through injury pullout or walkover.
"There's not much I can do about it," said the Swiss top seed. "From my end, I played well today.
"It was a solid performance. I'm looking forward to the finals, obviously."
Djokovic was added to a recent casualty list which also included Tommy Haas (Indian Wells walkover) and Nikolay Davydenko (quit in the second set of the Estoril final at the weekend).
"I've been waking up with some sore throat. But I thought it's not going to be anything," said Djokovic. "But against the number one, you obviously get a lot of balls back and have longer points.
"I just couldn't get enough energy back after each point. I needed a lot of time. And I just decided not to risk anything."
Nadal, a fighting-fit specimen, booked his place in a record-equalling fourth final in the principality - with victories at the last three editions - as he dominated Davydenko 6-3, 6-2.
"I am the first fourth in a row? I'm happy for that," said the Spaniard who owns a 5-1 record over Federer in clay finals.
"I'm happy for continuing to play good," said the number two, who lost the first Masters final of the season to Davydenko in Miami. "I've had a very good start of the 2008 season."
Federer and Nadal will face off in their seventh final on clay, with the Spaniard standing 5-1 in the series. Overall, Federer trails his world number two rival 6-8, one of the few losing records he owns.
Davydenko has pulled out of Barcelona next week to rest.
The Russian has been on court almost continuously since March 3 in Dubai and has finally decided he needs a pause before the Rome Masters which begins a week from Monday.
"The balls are heavy and slow, and the court is clay," said the Russian, fourth in the world. "I didn't hit so fast, but, I tried to play my best.
"Physically I was tired, really tired here. That's why next week is good, I don't play any tournaments."
Federer said that his clay game is progressing nicely after winning the Estoril title and improving over the course of this week.
"He's been impressive, no doubt. I think he's been playing excellent," Federer said of Nadal.
"There are only a handful of players who can really beat him on clay, he's that dominant.
"It's going to be an interesting match because I'm playing well again. I'm definitely going to have to use a better and a good game plan tomorrow than compared to last year where I thought I played pretty disappointing."
Nadal has not won a title since Stuttgart last July on clay while Federer is seeking his second in succession.
By Bill Scott, dpa