Nadal, who first won the French Open at 18 years old, cruised in the final two sets at Roland Garros. The Spainard is the first singles player to win 12 singles titles at one Grand Slam event, passing Margaret Court's 11 Australian Open titles.
Nadal collapsed on the court in jubilation after his victory and covered his shirt in red clay. He has won three consecutive French Open titles.
"It was a dream to play here for the first time in 2005," Nadal said in his on-court interview. "I never thought in 2019 I'd still be here. It's an incredible moment and very special for me."
Nadal began the interview by praising No. 4-seeded Thiem, who upset No. 1-seeded Novak Djokovic in Saturday's semi-finals.
"I feel sorry because he deserves it here too and I hope he wins here in the future," Nadal said. "He is a very hard worker."
Nadal beat Thiem in straight sets during last year's championship round.
"You're such an amazing champion," Thiem told Nadal on the court. "Such a legend of our sport. ... It's unreal and I'll try again next year, for sure."
Nadal is only two titles shy of tying Roger Federer for the most career major wins. Federer has 20 titles.