The Czech, who had also beaten Vekic en route to the title in Miami this year, was too strong for the Croat in the first set with Vekic struggling with her forehand.
Kvitova found herself a break down early in the second set but battled back from 5-3 and moved 6-5 up with an ace.
Vekic, who has shot up the rankings from 69th to 23rd this season following an Australian Open quarter-final spot and a title in Monterrey, forced a tiebreak.
She was beaten, however, with a thundering Kvitova forehand on the first match point.
Kvitova - Vekic highlights
FlashscoreKvitova's post-match comments
Flashscore