Shnaider eased through the first set but looked in trouble after relinquishing the second and had to defend three break points early in the decider, before going on to clinch victory in two hours and 18 minutes.
The 22-year-old has now won six straight finals on the WTA tour.
"I want to say thanks to and congratulate my coach, who is here with me, for achieving our first title this season," Shnaider said.
"It definitely means a lot, a great achievement and great finish of this season."
Fernandez was playing in her second straight final, after losing to world number one Elena Rybakina at the Ningbo Open last week.
"I would like to congratulate Diana. Congratulations. An amazing week, a great match. Congratulations to you and your team. Hopefully we can have many more battles like this one," said the Canadian, who won the Singapore Open in September.