The third seed - who had come through a three-set battle against Kiki Bertens on Sunday (AEST) - triumphed 6-3 7-6 (7-2) on clay, adding to her success at the Sydney International in January.
Kontaveit had her opportunities during a competitive contest, though, including wasting two break-point opportunities in the opening game of the match.
After exchanging breaks at the start of the second set, the Estonian manufactured two set points when 5-4 in front but both went begging, allowing a relieved Kvitova to hold serve.
The world number three quickly claimed a 6-0 lead as a tie-break was required, eventually securing victory after one hour and 31 minutes.
"I always need matches to get used to the clay," Kvitova said. "To be honest, yesterday I felt really bad in the first set. I turned it around, though, and from the very beginning today I was much, much better.
"The key to playing well today was winning yesterday. I have to say we both played well today - even if I had lost I would have said the same."