The 33-year-old Spaniard becomes the first player, man or woman, to win the same Slam 12 times after seeing off a brave challenge from a weary Thiem in a repeat of the 2018 final.
Nadal is now just two behind Roger Federer's all-time record of 20 majors and three ahead of Novak Djokovic who was knocked out by Thiem in the semi-finals.
The world number two also took his Paris record to an astonishing 93 wins and just two losses having previously won the title in 2005-2008, 2010-2014, 2017 and 2018.
"I want to say congratulations to Dominic. I feel sorry as he deserves to win it as well," said Nadal.
"But he has every chance in the future. He has unbelievable talent for the sport and I want to encourage him for the future.
"It's a dream to win again, an incredible moment. When I first played here in 2005 I never thought I would be still playing here in 2019.
"It's very special for me."
Sunday's triumph confirmed the 'Big Three' stranglehold on the Grand Slams having shared the last 10 between them.
It also gave Nadal an 82nd career title and 950th match win.
"It's very tough. I gave everything these last two weeks," said Thiem, who had seven fewer winners and seven more unforced errors in the final.
"Rafa, well done. You are an amazing champion and a legend in our sport.
"I am happy that you are playing. To win 12 times, it's unreal. I will try again, for sure."
Thiem would have felt confident going into the final having beaten Nadal on clay on his way to the title in Barcelona in April.
But with the exception of defeats to Robin Soderling in 2009 and Djokovic in 2016, the outcome of this year's tournament was brutally familiar.
"I am sorry as you are one of the best examples on tour," added Nadal.
"You are a hard worker, always have a smile on your face and are a good person. That's the most important thing.
"Thanks for being a great inspiration for me and small kids around the world.
- 'You'll win it one day' -
"If I wanted to lose to someone it would be you because you deserve it. Well done and keep going -- you will win this for sure."
In a 53-minute first set of brutal hitting and raw physicality, it was Thiem who broke first for a 3-2 lead.
But the 25-year-old's joy was short-lived as Nadal retrieved the break in the sixth game before racing away with the next three games to pocket the opener.
Thiem, who had beaten his opponent four times on clay in his career, failed to claim a single point off Nadal's first five service games of the second set.
However, the dogged Austrian pushed and pushed, forced Nadal into three rushed groundstrokes and, from nowhere, broke to take the second set.
It was the first set he had managed to take off Nadal at Roland Garros after three previous defeats.
Nadal was riled by the insult.
He swept the first 10 points of the third set, carving out a double break for 3-0 before sweeping to a third break for the set.
Thiem, bidding to become just Austria's second Grand Slam champion after Thomas Muster won in Paris in 1995, had played four successive days to reach Sunday's final and the toll was slowly telling.
He wasted break points in the first and third games of the fourth set and Nadal pounced to stretch to 3-0.
That was soon 5-1 and the relentless barrage continued with Nadal taking the title on a second match point when Thiem fired a return long.