Germany's Kerber sent the top-seeded Dane packing 6-4, 6-4 in a 98-minute final after Wozniacki had breezed through her home tournament without dropping a set.
She came into the Sunday's final with a 14-0 mark at the Copenhagen event, which she won in 2010 and 2011.
Playing in her first final of 2012, Wozniacki fell to 18-11 lifetime in championship matches.
Kerber, meanwhile claimed her second career title after also taking the Paris Indoors event in February. She had fallen to Wozniacki 7-6 (7-4), 6-3 in the second round of last year's event.