The ninth-seeded Li of China shook off the slow start to break Kerber three times in a dominant final set en route to a 1-6, 6-3, 6-1 victory over the fifth-seeded German.
It was Li's sixth career WTA title and first of the season.
Kerber, meanwhile, fell in a final for the second straight week after bowing to Petra Kvitova in Montreal last week.
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