Wozniacki, who was bidding for her third consecutive title in the Danish capital, was defeated 6-4 6-4 as she relinquished her home crown.
"I am very happy to win my second title [of the year]," said Kerber. "Caroline is a good player; it was a hard game. I used my entire capacity here today."
Kerber won her first WTA title of the season at the Paris Indoors in February.