Nadal claimed his 12th major with a 6-3, 6-2, 6-3 win over his Spanish compatriot who was playing in his first Grand Slam final at the age of 31 and at the 42nd time of asking.
It also gave Nadal his 59th win out of 60 matches played in Paris.
However, the 27-year-old's push to victory suffered a heart-stopping moment when a protestor, naked from the waist up, leapt from the stands on Court Philippe Chatrier, carrying a flare and protesting France's controversial same sex marriage law.
The protestor, who was wrestled away by security staff, came within just a few feet of the Spaniard as he prepared to serve at 5-1 in the second set.
A burly security official immediately came to Nadal's aid in front of the VIP box where Olympic sprint champion Usain Bolt and Hollywood superstar Leonardo DiCaprio were watching.
The drama, however, didn't alter the outcome as Nadal claimed his seventh title of 2013 after returning to the tour in February following a seven-month injury lay-off.
"Thanks to everyone in my family and team. Without their support, especially when I was out of action, this would have been impossible," said Nadal.
"Thanks also to everyone who sent me messages on Twitter and Facebook. They all gave me positive energy for today."
Ferrer vowed to keep fighting to break the Grand Slam stranglehold of Nadal, Roger Federer, Novak Djokovic and Andy Murray.
"I enjoyed the two weeks here. I congratulate Rafa, he's the best," said Ferrer.
"But I will try my best to have another chance to play in a final and win a Grand Slam. This tournament is very special to me."
Ferrer had raced through the first game to love, but it was the champion who broke first for 2-1 when his compatriot unleashed a wild forehand.
Ferrer, showing all the attributes which gave the nickname of 'bloodhound', was level in the next game at 2-2 and with both sluggers evenly matched, it was going to take something out of the top drawer to settle the opening set.
Nadal produced it right on cue, flashing a superbly controlled, sliding backhand on the move, from 10 metres behind the baseline, past the advancing Ferrer.
Nadal backed it up in the ninth game when a double fault from Ferrer handed him a set point which translated into the a first-set advantage when the veteran dumped a weak backhand into the net.
Ferrer hadn't dropped a set in the tournament and had spent six hours fewer on court getting to his maiden final.
But he was in serious trouble and he knew it, suddenly confronted by Nadal's record of 145 wins against just three losses when he had won the first set of a Grand Slam match.
Their personal history was also stacked against him with just four wins against 19 defeats coming into Sunday's final.
Sixteen of those losses were on clay and Ferrer's only victory on the surface was way back in 2004 in the pair's first meeting when Nadal was still a raw 16-year-old.
In no time at all, and with light drizzle falling, the champion was 3-0 ahead in the second set as a love-service game backed up a break which had been secured with a pair of sharp forehands.
Ferrer halted Nadal's six-game streak for 3-1 but was unable to convert four break points of his own in the fifth game, a marathon duel which included a 29-shot rally.
Nadal was 5-1 up and preparing to serve for the second set when a spectator, naked from the waist up, leapt from the stands carrying a flare just feet from where Nadal was standing.
The intruder, with the words 'Childrens rights' written across his chest, was wrestled away from the court.
The final had already been held up by protesters high up in the stands holding up placards demonstrating against France's same sex marriage law.
Nadal was broken but it made little difference to the outcome.
He hit back for 5-3 on Ferrer's fifth double fault and wrote his name into history when he unleashed another crosscourt winner.