The sixth seed blasted winners from both sides throughout the two-hour contest, winning a tight first set 7-3 in the tiebreak and then getting the only break of the second to secure his fourth title of the year.
Spaniard Nadal, still short of his best form after the knee and abdominal injuries that have disrupted his season, battled gamely in his first final since May, but always looked second best against the gutsy Russian.
Davydenko, the world number eight, sealed his fourth win in four finals this year when the Australian Open champion went long with a backhand, and a subsequent Hawkeye challenge ruled in the Russian's favour.
The 28-year-old bounced up and down in delight at his victory and then raced over to kiss his wife, who has been supporting him from the stands all week in Shanghai.
Davydenko may not be the most glamorous player in tennis but he has finished in the top five in the world for the last four years and beat Nadal in two sets in their last meeting in a Masters series final in Miami last year.
Sania loses
On Saturday, fourth seeded Francesca Schiavone defeated Sania Mirza 2-6, 1-6 in the semifinals.
This was the third time that Sania lost to the Italian, who is ranked 26 in the world.
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