Evenepoel of Quick-Step Alpha Vinyl held an advantage in excess of two minutes over Enric Mas (27) heading into stage 20 and faced little trouble in seeing out the day after his Spanish rival failed to close the gap despite finishing fifth.
"I don't know what's going through my head and my body right now. It's amazing," said Evenepoel, who was overcome with emotion after crossing the line in sixth.
"All the critics and the bad comments I received after last year, I think I answered with my pedals. I've been working so hard to come here in the best shape possible. To now win this Vuelta is just amazing."
The 181km ride from Moralzarzal to Puerto de Navacerrada, the last mountain stage in this year's race, witnessed a close contest between Carapaz and Sergio Higuita on the final climb but it was the Ecuadorian who accelerated away with seven kilometres to go.
"I was targeting this day, I knew it was very important. We knew it was a super hard stage because there were so many things at play, especially in the general classification," said the Ineos Grenadiers rider.
"I rode my way, being smart, making my moves when I had to. Then I enjoyed a lot of support from the breakaway riders. The truth is I'm very moved... to fight for the King of Mountains was one of my goals."
Team DSM's Thymen Arensman took second while Juan Ayuso of UAE Team Emirates crossed the line in third place.
The three-week race concludes on Sunday with a 96.7km journey from Las Rozas to Madrid in what is a largely ceremonial day on the bike.
Mas will finish the three-week stage race in second place whilst teenager Ayuso will round off the podium.
With Evenepoel's win, he becomes the first Belgian to win a grand tour since 1978, when Johan De Muynck won the Giro D'Italia.
