Kanepi, the fifth seed, had beaten Pennetta twice but never on clay and after losing the first two games of the match, things looked headed the same way.
But Kanepi came back to win the set 6-4 and never looked back as she stunned the defending champion.
“I’m very happy to win my first career title,” said 25-year-old Kanepi, who reached the Wimbledon quarter-finals last month after going through qualifying.
“This is the best moment of my career. After doing well at Wimbledon, now I’ve confirmed I’m playing really well. Flavia was playing well but today I was more aggressive in the most important moments.”
In 2008, Kanepi became the first Estonian to make it to the quarters of a major when she made the last eight of the French Open.
But she fell out of the top 100 this year before rebounding at Wimbledon.
She had lost both of her previous finals, at Hasselt in 2006 to Kim Clijsters and at Tokyo in 2008 to Caroline Wozniacki.
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