Kvitova, who was also the champion in Madrid in 2011 and 2015, has now won four titles in 2018 after triumphs in St Petersburg, Doha and Prague.
After capturing her 24th crown on the main circuit, the 28-year-old Czech said: "It feels sweet and weird as well. Coming from Prague last week, I didn't think I could be in the final in Madrid and winning trophies back-to-back. My body is exhausted as well, so I'm pretty surprised that my body handled it.”
The 10th seed added: "Every title feels great. Winning three times here in Madrid, it means something. It's not really happening every day, so I'm very proud of myself."
After her efforts in Madrid, Kvitova said she would skip the Italian Open in Rome next week in order to rest and prepare for the second Grand Slam event of the season on the clay courts at the French Open which starts on 27 May in Paris.
Bertens, the world number 20, disposed of the two time French Open champion Maria Sharapova as well as two players in the top 10 on her way to the final.
She squandered a 4-2 lead to lose the first set in a tiebreak. But she levelled the match following a break in the seventh game.
In the decider, Kvitova broke her service to led 4-2 but then promptly lost her own service to lead 4-3. Bertens, however, could not hold her serve to draw level at 4-4.
At 5-3 up, Kvitova was clinical. She did not drop a point on serve to take the set 6-3.
"Petra is also one of the biggest fighters out there, so it was tough," said 26-year-old Bertens. “I gave everything I had so I have no regrets."