Czech Kvitova, ranked 10th in the world, struck the first blow in a tense match which lasted two hours 52 minutes by edging the tie-break at the end of a gruelling 75-minute first set, taking advantage of a third set point when Bertens found the net.
The Dutchwoman had beaten Caroline Wozniacki and Maria Sharapova in a sparkling week in the Spanish capital to reach her first premier mandatory final and recovered well from surrendering the first set to take the second.
She led by a break in the third but let her advantage slip and Kvitova broke twice in a row to take a 4-2 lead in the decider.
Bertens broke back to make it 4-3 but lost her next service game and Kvitova served out the final game to love, sealing the victory when Bertens hit the tramlines with a backhand.
In doing so, she took her landmark third title, surpassing the two each won by Serena Williams and Simona Halep in Madrid, which established a women's section in 2009.
Twice-Wimbledon winner Kvitova was forced out of action for more than five months last year after her racket hand was stabbed by a burglar who broke into her apartment in December 2016.
But she has returned with a vengeance, winning the St Petersburg Ladies Trophy, the Qatar Total Open and the Prague Open this year before making history in Madrid.
