The 26-year-old Ljubicic improved his 2006 record to 13-1. He will be after his fifth career singles crown in the championship match.
Koubek, who has won three career titles, is 3-2 all-time against Ljubicic. The two last met at a tournament in Basel, Switzerland, in 2004, with Koubek winning in three sets.
The winner will pocket $53,335.