Knowing the winner would advance, Davydenko's defense and relentless groundstrokes were the difference, turning an expected tight match into a rout. He broke Del Potro's serve four times in eight chances.
"Today, I played so good,'' Davydenko said. "I feel great.''
Earlier, Jo-Wilfried Tsonga of France beat Novak Djokovic of Serbia 1-6, 7-5, 6-1. Djokovic had already been assured of a spot in the semifinals of the season-ending tournament, while Tsonga had been eliminated.
Del Potro was unable to put much pressure on his Russian opponent in the first set, connecting on only 42 percent of his first serves.
Serving while trailing 4-3, Del Potro double-faulted to set up break-point. Davydenko put away a forehand winner off a short ball for the game, then held at love for the set.
After Del Potro held to start the second set, Davydenko won five straight games, leaving the Argentine looking increasingly frustrated. Del Potro held to get to 5-2, but Davydenko finished it off by holding at love, with Del Potro netting a second-serve return on match point.
Del Potro said he didn't see the ball well, was moving slowly and never found his rhythm. But he was still happy about his performance this year - rising into the top 10 - and looking forward to next week's Davis Cup final between Argentina and Spain.
"I'm living a dream,'' Del Potro said.
Tsonga, who lost to Djokovic in this year's Australian Open final, looked listless before coming alive and winning five consecutive games from 5-5 in the second set to take control.
"He was better than me in the two first sets, but I take the second one,'' said Tsonga, who has beaten the third-ranked Serb the last three times they have played. "It was a holdup.''
Tsonga was unusually subdued early in the match, showing only flashes of the form that carried him to the Paris Masters title - an event he had to win to qualify for the Masters Cup.
Djokovic, continuing his efforts to close in on Rafael Nadal and Roger Federer at the top of the rankings, broke Tsonga twice while finishing the first set in only 25 minutes.
Tsonga pulled himself together in the second set, saving two break-points while serving at 2-2, then finally broke through as Djokovic served while trailing 6-5. The Serb had four unforced errors in the game, sending a forehand long on set point.
Another four mistakes handed Tsonga an early break in the third set. Tsonga broke again, at love, to take a 5-1 lead, then held at love, flicking a lob winner on match point.
"In the third set especially, he played well,'' Djokovic said. "I made some unforced errors. The important thing is that I'm through.''
Federer, a four-time Masters Cup champion, will advance if he wins Friday. He faces Andy Murray of Britain, who is 2-0 in the Red Group and already has guaranteed himself a place in the semifinals.
Gilles Simon of France still has a chance if Federer falters. He will play 26th-ranked Radek Stepanek, who replaced Andy Roddick when the American pulled out Wednesday with a sprained ankle.
Simon got into the elite field when Nadal withdrew before the tournament began with a sore knee. The Frenchman then defeated Federer in his first match.
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