Things looked good for the home support in China as Zhang Shuai led by a set and 2-0 but Jovanovski, who came back from a set and 5-3 down in her semi-final against Johanna Larsson, repeated the trick to win 6-7 (7/9) 6-4 6-1.
The 21-year-old Serb, who was the top seed for the tournament, told wtatennis.com: "I was maybe just a little bit better and had a little bit more power in the end. But she played great.
"Zhang Shuai is a great player - she played great this week and the tournament before in Guangzhou too.
"I think it was a really difficult match today. It's really tough to play against a friend. I was just trying to be fair on the court and play my game, and I'm happy to win this title."
Zhang had won her maiden WTA Tour title in Guangzhou last week and saved a set point in the tie-break to take a one-set lead in Ningbo.
She broke at the first opportunity in the second but Jovanovski then took 12 of the next 15 games to win the match.
Zhang at least had the consolation of winning the doubles title with Yung-Jan Chan of Chinese Taipei, the top-seeded pair seeing off Irina Buryachok and Oksana Kalashnikova 6-2 6-1 in the final.