Nadal got off to a dream start, pocketing the first six points of the match as he broke Thiem in the second game to open up a 2-0 lead.
His lead was reminiscent of their semifinal at the French Open past year, when Nadal also held the early advantage.
Up a break at 2-1 in the third set, Nadal stopped serving after a fault because he couldn't straighten his left middle finger. At the following changeover, he was given a salt pill by a doctor and had his left forearm massaged by a trainer.
Still, Nadal was able to complete the job on court Philippe-Chatrier.
Thiem put up a good fight in his opening service game of the third set, saving four breakpoints.
"Yes, and it's going to take probably one or two more years", said Gunter Bresnik, Thiem's coach.
Nadal celebrated in relatively low key fashion, but then there is not much novelty value in this.
It's incredible, I can't describe my feelings.
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In a world bustling with ball-maulers yearning to topple euphorically onto Roland Garros clay or merely stand and raise the arms skyward in triumph just once in life, Rafael Nadal did so Sunday for a preposterous 11th time, even while choosing the standing option for only the second.
Nadal is now the first player in the Open Era, male or female, to win the same Grand Slam tournament 11 times, a feat that has been dubbed La Undécima, after Real Madrid's bid to win an 11th European Cup.
"What you did and what you are doing is the most outstanding thing an athlete can achieve in sport", the 24-year-old said.
Nadal's introduction included a year-by-year accounting of every time he'd already won the title at Roland Garros.
But the Austrian freed his shoulders and broke back in the third game with forehand victor - pumping his fists in the direction of coach Gunter Bresnik.
Whatever the problem, his dominance remained and a love game took him to 4-2 before he eventually sealed victory on a fifth match point when the Austrian fired another backhand long.
Another feature was his ridiculously slow play when serving, nearly always over the 25-second limit and sometimes going well into the thirties. But from 4-all in the opening set, Nadal grabbed five games in a row and was in charge.
Thiem decided early on that he was not going to die wondering, attacking aggressively from behind the baseline, leading to a plethora of unforced errors.
Nadal, however, averted danger with a pass after dragging Thiem in with a deft drop-shot.