The world number 62 prevailed 6-1 4-6 6-1 to claim the $250,000 prize money ahead of her Czech opponent, who began the day 27 places higher in the WTA rankings.
Nara got off to a flying start in the match, winning the first five games before her opponent saved three set points to finally hold her serve at the third attempt.
Zakopalova survived another three set-point opportunities against her in the next game, before Nara took advantage of her fourth to get her nose in front.
The second set was a much more even affair, with Nara breaking her opponent three times, only for the Czech to break back immediately on each occasion.
Zakopalova made the crucial breakthrough in the 10th game, breaking the Japanese to ensure that the match went to a deciding set.
Unfortunately for the Czech, the third set went much the same way as the first as Nara reeled off five straight games from 1-1 to storm to victory and clinch her first WTA crown.