In the final, the fourth seed beat Slovakia's Dominik Hrbaty, 6-1, 6-2, 6-2.
He won a first prize check of $480,000 for his fifth ATP title of the year.
Before Sunday, the 25-year-old Davydenko also was a three-time runner-up in the 2006 season.
"It feels amazing," he said. "Making a semifinal or final is OK, but nobody really cares. But if you win the title, the first Masters Series title of your career, that's completely different. Winning the first Masters title at the end of the year is very important for me."
In this match, Davydenko made only 11 unforced errors, converted six of 13 break point chances, and hit 31 winners to just 11 by Hrbaty, who last earned a title at Open 13 tournament in February 2004 at Marseille, France.