Berdych jumped out to a two-set lead and eventually had enough to hold off Ljubicic, who beat Andy Roddick in Saturday's semifinals.
Berdych, 20, who was also a finalist in Bastad earlier this year, won his first ATP singles crown of 2005 and the second of his career to pocket the winner's check of $454,000.
The 26-year-old Ljubicic, who lost in the first round last week in Lyon, France, claimed titles at Vienna and Metz earlier this year and fashioned a 16-match winning streak before the loss at Lyon.
He already qualified for the season-ending Masters Cup in Shanghai, and was in search of his third ATP singles title of the season.
This was the last of nine Masters Series events in 2005.