The 33-year-old Spaniard claimed a 6-3, 5-7, 6-1, 6-1 victory over thee fourth seed, becoming the first player, man or woman, to win the same Slam 12 times.
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.
But the world No 2 hailed Thiem as a champion of the future.
"I am sorry as you are one of the best examples on tour," said 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.
"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."
Thiem, bidding to become Austria's second Grand Slam champion after Thomas Muster win in Paris in 1995, cut a weary figure towards the end of the three-hour final.
The 25-year-old was playing for a fourth successive day.
On Saturday, he had needed five sets to defeat Djokovic, ending the world No 1's 26-match winning run at the majors.
"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."
At least Thiem could be consoled by seeing his girlfriend Kristina Mladenovic winning the women's doubles title with Timea Babos earlier Sunday.
"12th RG titles is absolutely unreal! Very proud to see Domi standing next to this legend of our sport!Your turn is coming soon," tweeted the French player.