Nishioka, 23, entered the tournament in China as a qualifier but defeated seeds Denis Shapovalov and Fernando Verdasco on the way to his first-ever ATP Tour final. He becomes only the sixth player to win an ATP Tour event as a qualifier.
The Japanese player, who is ranked 171st in the world, found the decisive break of serve in the fifth game of the third set before holding in the final game to win the championship.
Frenchman Herbert, who was also competing in his first Tour final, saved three championship points as he trailed 5-3 in the final set but was unable to break his opponent in the following game.
Nishioka was injured for much of last season after suffering a torn ACL at the Miami Open in March 2017.
"It has been 10 months since I returned, but I think that is actually quick to get to this point," Nishioka said after his defeat of Verdasco in the semifinals
"I think my level is better than ever. It's no surprise to me, but I do feel lucky to get here."