Ferrer captured the event for the third consecutive year and for the fourth time overall.
He needed 78 minutes to produce a 7-6 (7-5), 6-1 victory. It was the 19th ATP championship of his career, seven of which came last year.
Ferrer is ranked fifth in the world but will be seeded fourth at next week's Australian Open due to the absence of Rafael Nadal.
Kohlschreiber served for the first set at 5-4 and was a point away from winning the set before Ferrer rallied to force the tiebreaker.
Ferrer will begin the Australian Open by taking on Olivier Rochus. Kohlschreiber, who won in Auckland five years ago, will be the No. 17 seed in the season's first major championship.