The second-seeded Cypriot, who earned his third career victory over Ljubicic, had to work hard for every point in the two-and-a-half-hour final. He saved three set points in the opener and won the set on a tie break.
Ljubicic, last year's winner here, broke Baghdatis to take a 3-2 lead in the second set and calmly held on to his serve to level the score.
The third set went with serve until the final game, when several errors by the Croatian gave Baghdatis his first tournament title this year.
