"You were asking for titles. Finally I have a title," Nadal told reporters. "Here we are. Important title, important moment."
It marked the first time in an Open Era-record 54 meetings, and in their 142nd set against each other, that Nadal won a set against Djokovic without conceding a game — otherwise known as a bagel.
In all, Nadal had a career-high four bagel sets in this tournament.
"I played a great first set in all aspects. No mistakes. Playing so aggressive, changing directions," Nadal said. "It's not usual and probably will not happen again."
The timing for Nadal's return to form could not have been more opportune, as he will seek a record-extending 12th title at the French Open starting next weekend.
"Winning a title is important but for me the most important thing is (to) feel myself competitive, feel myself healthy," Nadal said. "Then with the feeling that I am improving. I know if I'm able to reach my level you can win, you can lose, but normally I'm going to have my chances — especially on this surface.
"Now is the moment to keep going," Nadal added.
In the women's final, Karolina Pliskova captured the biggest clay-court trophy of her career by beating Johanna Konta 6-3, 6-4.
Top-ranked Djokovic, meanwhile, appeared exhausted after spending more than 5 ½ hours on court against Juan Martin del Potro and Diego Schwartzman the previous two days.
Djokovic was also coming off the Madrid Open title last week.
"I don't want to talk about fatigue or things like that," Djokovic told the crowd during the post-match ceremony. "Rafa was simply too strong today."
Speaking to reporters later, Djokovic said, "I was just running out of fuel a little bit today. Just kind of missed that half a step, especially on the backhand side."
The Foro Italico crowd continually tried to encourage Djokovic with chants of "Vai Nole!" — Go Nole! — but the top-ranked Serb struggled with his overhead and drop shots.
Midway through the second set, Nadal chased down a lob with an over-the-shoulder shot and Djokovic's ensuing overhead landed in the net to conclude a long point.
Djokovic again netted an overhead in the next game and then kicked the ball in frustration when he missed a drop shot attempt late in the second.
But Djokovic hung around in the second and converted his first set point when a looping forehand from Nadal sailed wide for his first break of the match. As he walked to his chair after winning the second set, Djokovic waved his arms to get the crowd behind him.
However, Djokovic didn't have much left in the tank.
When Nadal pushed Djokovic deep into the corner in the opening game of the third set and Djokovic's desperation lob sailed long to hand Nadal a break, Djokovic smashed his racket to the clay three times in frustration and received a warning from the chair umpire.
Djokovic won only 29 percent of the points on his second serve and committed 39 unforced errors to Nadal's 17. Also, Nadal won 23 of the 31 rallies with nine or more shots.
PLISKOVA NO. 2
Pliskova's victory will move her up to No. 2 in the rankings and makes her one of the contenders for Roland Garros.
"I just hope to take the tennis I was playing here to Paris," Pliskova said. "For sure there's going to be a chance for me if I play this way."
The 2016 U.S. Open runner-up, Pliskova also reached the Australian Open semifinals and the Miami Open final after opening this season with a title in Brisbane, Australia. But she lost in the second round of her previous two tournaments on clay in Stuttgart, Germany, and Madrid.
"Nobody really gave me chance for this tournament — even me," Pliskova said. "Before the tournament, I was not super confident, not thinking about the final at all. I was just happy with every match which I played. So it's little bit like a miracle for me."
The unseeded Konta appeared nervous at the start, double faulting then landing a backhand into the net to hand Pliskova a break in her opening service game.
In the second set, Pliskova used a swinging forehand volley putaway to break for a 4-3 lead and never looked back.
"It's always tough playing Karolina," Konta said. "There's rarely really a rhythm to the match. She plays with big shots, quite flat, and big serves. It can feel sometimes you're fighting an uphill battle. That was the case today."
Pliskova attributed a lot of her success to Conchita Martinez, the four-time Rome champion who she recently named her head coach.
"She loved clay so she knows exactly what I should do," Pliskova said of Martinez. "There were small differences: movement, maybe to put more topspin on the balls, use drop shots — which I never use, but I start little bit, and to mix also the serves. ... I know she loved this tournament. I think she prayed so I could win today."