The world number one was forced to work hard but ultimately had too much for the Briton and wrapped up victory after three hours and 17 minutes when Murray netted a forehand.
"I'm happy to be back here," said Nadal, who will face third seed
"Andy is a fantastic player, he deserves to win a Grand Slam very, very soon.
"Now I'm going to play the best player of the moment or the best player in history. But the most important thing is to be there."
Murray was a presence in the match throughout and will rue a failure to make things more competitive, failing to take advantage of his numerous chances and converting just three of a whopping 18 break points.
"I had a lot of break opportunities but he played them well. He was able to dictate the points with his forehand," said Murray.
"I think I'm much better on clay than I was last year."
Nadal, the top seed who can equal Bjorn Borg's record of six French Open titles if he lifts the trophy on Sunday, made a blistering start to the match, quickly racing out to a 5-1 lead.
After trading opening service holds, the Spaniard earned the first break points of the match in just the fourth game and, although his first chance went begging, he was quick to secure a second opportunity before rifling a forehand passing shot down the line to sneak ahead.
With the early match nerves released, Nadal worked Murray around the court, earning himself a second break just two games later when a defensive lob down the line drifted wide from the Brit.
But just when Nadal looked to have the set wrapped up, serving for it at 5-3, Murray stormed back into contention with a break and a hold that left him trailing by just the one game again.
Murray also held break-back points in the 10th game, when Nadal served for it for a second time, but the Spaniard this time managed to stop the rot and went on to take the first set with a forehand winner after an hour and two minutes.
The second set was equally topsy-turvy, both men holding serve with ease the first four times before four straight breaks kept the crowd enthralled.
Nadal twice eked out a marginal lead but both times Murray came back at him immediately as the two men struggled to hold serve in the increasingly gusty conditions.
Again it was Nadal who snuck out in front when he broke for a third time, in the 11th game, with yet another forehand winner.
And this time the Spaniard was able to make his advantage tell as he promptly served out the set to love, landing another forehand winner down the line.
Nadal dealt a further blow to the Murray spirit in the first game of the third set when he broke again; a looping forehand pushing the Brit back behind the baseline before an easy cross-court forehand winner sealed it.
From there it looked as though the Spaniard, whose only loss at Roland Garros was to Robin Soderling in 2009, had the match wrapped up as he held serve without too much trouble.
Murray had one last chance to try and get back into the match, enjoying yet more break points in the eighth game.
But Nadal, celebrating his 25th birthday, saved all four of them, holding with a forehand winner, before going on to serve out the match to love two games later when Murray netted a running forehand.