Cibulkova entered Sunday's match with an 0-3 record in WTA finals, including a loss to Petra Kvitova in last week's Linz title match. But she broke through against Kanepi, earning a 3-6, 7-6 (7-1), 7-5 victory in two hours, 36 minutes.
The eighth-seeded Cibulkova, 22, pulled out the win by saving 8-of-11 break point chances. She had lost to Kanepi in two previous matches -- a matchup in Sydney in 2008, and a quarterfinal in Paris earlier this year.
But Kanepi dropped Sunday's match after having mixed results with her strong serve. She fired 10 aces and won 75 percent of first-serve points, but got her first serve in play only 53 percent of the time. When going to a second serve, Kanepi double-faulted five times and won only 44 percent of the points.
Kanepi fell to 1-3 in WTA title matches. Her lone title came in Palermo last year.
Cibulkova earned $118,000 for the victory.