It was a repeat of last year's final and, although Thiem managed to win a set this time, he was unable to join Robin Soderling and Novak Djokovic as the only men to beat Nadal at Roland Garros, going down 6-3 5-7 6-1 6-1.
Nadal now stands on his own as the most successful singles player, male or female, at a single grand slam having moved clear of the 11 titles won by Margaret Court at the Australian Open.
His 18th slam title overall, meanwhile, means for the first time he has closed to within two of his great rival Roger Federer, whose all-time men's record of 20 titles appears increasingly within reach for either Nadal or Djokovic.
Thiem was trying to do what only Stan Wawrinka has managed by beating Djokovic and Nadal at the same slam, and Wawrinka did not do it back-to-back.
As if he did not have the odds against him enough already, the Austrian was also playing for the fourth day in a row after his epic two-day semi-final win over Djokovic, while Nadal had had a day off either side of a comfortable semi-final win over Roger Federer.
Thiem knows how it feels to beat Nadal on clay, having done so in each of the last four seasons, but only in best-of-three-set matches.
The first seven games were a physical war, both men growling and pummelling the ball back across the net with ever increasing vigour.
Thiem struck first with a break for 3-2, being rewarded for his aggressive play, but Nadal hit straight back and the crunch moment of the set came when he held after an epic seventh game.
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Thiem threw everything in his armoury at Nadal, fizzing in backhands and covering every inch of Philippe Chatrier's clay, but it was not enough.
It was no surprise to see Thiem fail to hold his serve in the next game, and Nadal served out the set to put himself in a position from where he had never lost a match at Roland Garros.
It could have been deflating for his opponent, but Thiem put some extra oomph on his serve, closed in on the baseline and got the easy points he so desperately needed.
Nadal was holding even more comfortably on his serve, dropping just one point in the first five games of the second set.
But in the sixth game, two unexpected unforced errors from Nadal showed that even the best are not immune to nerves.
Thiem read the situation brilliantly, keeping Nadal deep and making him do the work, and he got his reward with a break to take the set.
Just winning a set against Nadal here is a significant achievement, but the job was nowhere near done for Thiem and the mountain he still had to climb quickly became clear.
A poor opening game of the third set from Thiem set the tone, and in no time the 25-year-old was 4-0 down having won just a single point.
He at least got on the board, but it appeared the Austrian had given everything he had and his movement became increasingly laboured.
He roused himself again at the start of the third set but was unable to take break point opportunities in either the first or third games and found himself 3-0 down.
He did superbly to recover from 0-40 to hold serve in the next game, but that turned out to be a last stand as Nadal wrapped up victory after three hours and one minute.
The 33-year-old fell flat on the clay as Thiem's final shot landed just beyond the baseline, the king of Roland Garros once more.