Stepanek, of the Czech Republic, scored a 3-6, 6-3, 6-4 victory over the Spanish player.
"It's my third title and my first tournament of the new season," Stepanek said. "I have the trophy, so I can't find the words right now. I'm very happy with the way I played this week."
Stepanek has defeated Verdasco all three times they have met in ATP events.
Verdasco said it was tough to lose but "good preparation for the Australian Open," which begins Jan. 19.
"I really have a lot of confidence now. With a bit more rhythm and practice next week, I will be in good shape for the Australian Open," the Spaniard said.