Nadal, competing in his eighth final in a row since returning from a seven-month injury lay-off in February, raced to a crushing 6-1 6-3 win in one hour and nine minutes to claim his third straight title and sixth of 2013.
It was the first time the pair, who have won 28 grand slam titles between them, have met in a final since the 2011 French Open, an encounter Nadal won, and the fifth seed showed his great rival no mercy again.
The clay court master was at his clinical best, converting five out of six break-point opportunities, while the Swiss had to settle for one out of two.
Federer accepted he could not live with his dominant opponent, telling the ATP website: "It didn't go how I hoped and I was missing too many easy forehands and crucial points.
"He does an incredible job returning form the back of the court and it is hard because he covers the court so well. You need to serve accurately. When Rafa is at his best he creates opportunities in rallies and dictates. It was difficult to change."
Nadal's win took their head-to-head record to 20-10 in his favour.
In the women's final, world number one Serena Williams was an equally emphatic winner as she dispatched Victoria Azarenka 6-1 6-3 to claim her fourth straight title - but still refused to get carried away by her French Open hopes.
The American crushed her third-ranked opponent in one hour and 33 minutes to continue her ominous form.
It was Williams' 24th consecutive win on the WTA Tour and saw her add to the titles she has won in recent weeks in Miami, Charleston and Madrid.
The Belorussian simply had no answer to her opponent, who carved out 16 break points, taking six of them, as she dominated the Azarenka serve.
It means Williams will head into Roland Garros, where she has not got past the last eight since 2004, in the best possible form.
She said: "The first three games took about 20 minutes - it wasn't easy, nothing is ever easy. I think the difference today was I took the opportunities when I had them and came up with some good shots.
"And this was the best I've moved all week - I feel fit and hopefully it'll stay like this.
"Last year I was feeling excellent but didn't do that great at Roland Garros - this year I'm cautious and I want to work hard and stay focused and win every point I play, and not slack at all."
Azarenka added on the WTA website: "We had a lot of tight games and the match was closer than the score, but Serena played a very good match and was better in the important moments.
"She was just better than me today. She's playing incredible tennis, maybe she's at her best level for the last year and a half or so."
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