Federer started the year with a win over the 25-year-old at Doha; the loss in two hours, 42 minutes was the third this season in a final for Ljubicic, beaten a week ago in Marseille by Swede Joachim Johansson.
Federer, playing for the first time since losing in the Australian Open semi-final to Marat Safin, has not been beaten in a tournament final since July, 2003, when Jiri Novak stopped him on clay at Gstaad.
The Swiss improved to 15-1 this season as he lost his serve for the first time this week at the hands of Ljubicic in the first set.
Federer takes away a cheque for 147,000 euros as he heads to Dubai to headline next week's ATP event along with Andre Agassi and Safin. The Swiss winner struck a dozen aces, 42 unforced errors and 28 winners as he defeated Ljubicic for the fifth time in eight meetings.