The 18-year-old broke her Fed Cup teammate's serve twice in the first set before powering away from her more experienced rival in the second set. It was the first all-Czech WTA final since 2005.
Benesova, ranked No. 41, reached the Hobart final in 2006 and was trying to win her first WTA tournament in five years. Her one title came in Acapulco in 2004.
Kvitova and Benesova share coach David Kotyza, who was not seen court-side during the match after saying he would not be able to watch if both his players reached the final.
Kvitova and Benesova also shared a hotel room in Hobart.
"I don't know if I can call her a friend anymore," Benesova joked with the crowd. "We are sharing a room but I think I will kick her out tonight."