Nakashima took just 80 minutes to win 4-3 (5), 4-3 (6), 4-2, securing the title on the first of three championship points when Lehecka sent a forehand long.
The fourth-seeded Nakashima won all five of his matches at the year-ending tournament for 21-and-under players, including a straight-set victory over Lehecka in the group stage.
"It's been a great season for me. I've definitely learned a lot with every match, with every tournament," said Nakashima, who won his first ATP title in his home city of San Diego in September.
"Of course at the beginning of the year I had some goals, to win my first ATP title and to be able to do that in San Diego was super special. To finish off the year here with the title at the Next Gen is super special. I think the whole year for me has been very consistent."
Nakashima had to recover from being down 3-1 in the opener and also faced two set points in the second-set tiebreaker.
"I think in those pressure situations it all comes down to your mental game," he said. "It's about staying calm in those moments, of course there's going to be some nerves sometimes but you just try to manage as best as possible.
"I think in those pressure situations I'm pretty good this year."
Lehecka was out for revenge as well as the title and broke Nakashima's serve in the first game. But Nakashima broke back in the sixth game to take the set to a tiebreaker, where the American raced into a 5-0 lead and went on to take the set.
Lehecka threatened to start the second set in similar fashion but Nakashima managed to save two break points early on.
Indeed the next break of serve was to prove the most important as it came in the final game of the tournament.
"It was a tough match. Brandon was playing very good tennis this week," Lehecka said. "He deserved to win; he was playing the best tennis out of everyone here.
"I'm sad I didn't take at least one set today, I was a break up in the first, I had two set points in the second, so this feels kind of unlucky ... He was more solid in the crucial moments, that's how I would explain today's loss."
It was Nakashima's second appearance at the Next Gen Finals, having lost to compatriot Sebastian Korda in the semifinals last year.
This is the fifth edition of the Next Gen ATP Finals, which has featured shorter sets of first-to-four games and other experimental format changes. New rules included no changeovers after the first game of each set and only one sit-down per set after three games; a 15-second serve clock after aces, double-faults and unreturned serves; and coaching during an opponent's medical timeout or toilet break.
Current No. 1 Carlos Alcaraz won last year's edition.
"This tournament is great. I think it's great that all the young, up-and-coming players come together and compete in a nice, fun format," Nakashima said. "I think it really exposes the younger generation well, so I think it's a great stepping stone for the ATP tour.
"To be on that list with all the past champions I think is a great achievement and we just have to keep working hard and look forward to next year."