It is the third title of the 21-year-old's career, and her first since winning at Monterrey in March 2022.
The win will also move her back inside the top 50 in the world rankings when they are updated next week.
"We had a very, very hard past couple of years," Fernandez, who reached the final of the US Open in 2021, said.
"My family, my parents, my coach, and my performance coach stayed by my side.
"They motivated me to keep going and the hard work is paying off. Hopefully, we can keep going this way."
It was a nervy start by Fernandez and No.85-ranked Siniakova earned two breaks to claim the opening set.
Fernandez, currently ranked 60th, responded by building a 4-0 lead in the second before the Czech player took an off-court medical timeout and returned with her upper left leg taped.
The break appeared to help Siniakova as she worked her way back to 3-4 but Fernandez saved six break points in a 10-deuce game to hold and then took the set.
After exchanging breaks through the decider, Fernandez made the decisive move to lead 5-4, holding her nerve and serve to round out the win in two hours, 49 minutes.
Chinese No.1 Zheng Qinwen dropped the first set but recovered to beat seventh seed Barbora Krejcikova 2-6 6-2 6-4 in the final of the Zhengzhou Open.
After sharing the first two sets, the 24th-ranked Zheng made the decisive break in the ninth game of the decider and then calmly held serve to claim her second title of the year after also winning at Palermo.
"It's a lot of pressure, you could see in the match," Zheng, a quarter-finalist in this year's US Open, said.
"In the first set, I was leading 2-0 (then) I lost six games in a row.
"There were a lot of ups-and-downs, but in the end the important (thing) is to win the match, whatever happens."
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