Youzhny, 25, who was seeded fourth, took control immediately and never let up, beating Nadal for the fourth time in the 10 matches they have played.
Nadal had advanced to the final with a nearly four-hour, three-tiebreaker win over countryman Carlos Moya.
"I am very happy with this title but I did not play against Rafael Nadal today," Youzhny said. "He was dead and could not move. I have to thank Carlos for keeping him on the court for four hours last night. I really can't say much more about the final, bad luck for Rafa.
"This week I started slowly, but then played better and better, round after round. It is a great start to 2008."