Davydenko, who was seeded No. 6, scored a 7-6 (7-3), 6-3 victory over the Spaniard and collected $616,500.
"I think a little bit was luck, but mostly I was playing very well today," Davydenko said.
The win was Davydenko's 18th on the tour. He has a 3-4 career record against Nadal.
Davydenko also won events in Germany, Croatia and Malaysia this year.
"I don't like to lose, but I had my chances," said Nadal, a former world No. 1 with 36 ATP wins. "He beat me. He played ... very good match. Just congratulate him, because he deserved the victory."