Nadal broke the men's record for match wins at Roland Garros, where he improved to 59-1, with his lone defeat against Robin Soderling in the fourth round in 2009.
For fans enthralled by Nadal's semifinal victory over top-ranked Novak Djokovic, Sunday's final may have seemed anticlimactic. But not for the champion, who hit a fallaway forehand winner on championship point, then tumbled to the clay he loves and covered his face to hide his emotions.
Nadal's path to the Roland Garros title was more arduous than usual. He fell behind in each of his first three matches and needed a fifth-set comeback to beat Djokovic.
And the latest title was especially sweet for the Spaniard because of his comeback after a seven-month layoff because of knee trouble. Since returning in February, he's 43-2 with seven titles in nine tournaments, and he has won his past 22 matches.
With his 12th Grand Slam title, Nadal moved into a tie for third place with Roy Emerson behind Roger Federer's 17 and Pete Sampras' 14.
Protesters tried to delay the final in the second set. One man jumped onto the court near Nadal with a fiery flare spurting white smoke, and security personnel pushed the protester to the ground and quickly dragged him away.
Other protesters also brandishing red flares climbed to the top of nearby Court Suzanne Lenglen and unfurled a banner calling for the resignation of French President Francois Hollande.
The interruptions were brief, and there was no stopping Nadal. He has lost a total of 16 sets in nine years at Roland Garros and was never in danger of doing so against Ferrer.
Both finalists grinded away from the baseline, with one rally lasting so long fans began to buzz, then started to shush each other.
The 5-foot-9 Ferrer, who was playing in his first Grand Slam final at age 31, often wins points by extending them with his dogged defense. But Nadal matched his retrieving skills, and the torque on his groundstrokes eventually had Ferrer reeling.
Trophy presenter Usain Bolt watched from the front row wearing sunglasses, even though the day was gray with occasional drizzle.
Nadal misfired more than usual in the early going, perhaps adjusting to slow conditions and feeling the effects of his 4½-hour win over Djokovic. He gave back an early service break and had to erase two other break points in the opening set.
It was the first set Ferrer had lost in the tournament, and at that point, he knew he faced a daunting task. Nadal is 146-3 when he wins the first set in Grand Slam tournaments.
Nadal broke again early in the second set, and then came Ferrer's best chance to reverse the course of the match. At 3-1 he had four break points, but Nadal erased them all, the last with a backhand winner to end a 31-shot rally, longest of the match.
In the final set, Ferrer double-faulted for the fifth time to lose serve and fall behind 5-3, and Nadal needed only five more points to close out the victory.
Nadal broke the record for most men's victories at Roland Garros he had shared with Federer and Guillermo Vilas. He improved to 20-4 against Ferrer and has won 17 consecutive meetings on clay.