Last year's beaten finalist Davydenko won 6-3 6-4 in an hour and 24 minutes to claim the season-ending title, contested by the world's top eight players.
The win meant Davydenko jumped up the rankings to finish the season as world No6. Del Potro remains at No5.
The Russian scooped $1.51-million in prize money, while the Argentinian collected $740000.
Davydenko became the first Russian to win the season-ending men's tournament.
"Coming here as No7 and winning the tournament, I surprised myself," said Davydenko, who downed the Australian Open, French Open, Wimbledon and US Open champions en route to claiming the title.
Del Potro told him: "Congratulations, you had a great, great week, you beat everybody, you are a great, great champion."
In the doubles, Americans Bob and Mike Bryan beat Max Mirnyi and Andy Ram 7-6 6-3 to regain the end-of-season No1 ranking.
The US duo were pushed all the way in the first set by the Belarus-Israeli pairing, taking it on a tie-break, before sealing the win with a solitary break in the second.
Victory took the Bryan brothers ahead of Daniel Nestor and Nenad Zimonjic in the doubles standings.
"It means so much," Bob Bryan said. "It's pretty much what we play for now ... The ultimate goal is to finish number one."
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