Goosen, the reigning U.S. Open champion, hit a 5-iron within eight feet at the par-5 18th hole and Els, a two-time U.S. Open winner, made the putt to forge a four-way tie for the lead at 24-under 264.
The four-way playoff involved South Africa, the Danish duo of Thomas Bjorn and Soren Hansen, the New Zealand tandem of Michael Campbell and David Smail and defending champions Tiger Woods and David Duval of the United States, who also closed with an eagle.
But the Americans quickly lost their magic at the Taiheiyo Club as Duval missed a birdie putt at the first playoff hole that put him and Woods on the sidelines with New Zealand.
"We really didn't play all that well today until the very end, when we got on a little run to get into the playoff," Woods said.
Campbell and Smail had the lead after the second and third rounds, but they never recovered after Smail sent his tee shot into a fairway bunker at the first sudden-death hole. The Kiwis could have avoided a playoff with a birdie at the 72nd hole.
"It's a shame because it really wasn't a bad spot," Smail said. "I think we just sort of didn't quite do it."
At the second playoff hole, the par-4 14th, Bjorn missed a 10-footer for par, but Goosen nearly eagled and Els tapped in for the $1 million first prize.
"We were just lucky that two teams fell out on the first playoff hole and that there was only two of us," Goosen said. "Once Thomas hit the bad drive on 14, I knew this was my chance. If I could hit a good drive down there, we might get away with winning the hole."
Winning in a playoff is nothing new for Goosen or Els, although sudden-death was. Both captured U.S. Open titles in 18-hole playoffs.
"I think Retief is very good in playoffs. He has a competitive mind," Els said. "I've been in quite a few playoffs since '94 and I think I've only won one or two since then. I lost a playoff about two weeks ago at the Tour Championship, so it was nice coming through."
Of the four playoff participants, Denmark had the best final round at 7-under 65. Els and Goosen combined for a 66, Woods and Duval rallied for a 67 and Campbell and Smail carded a 70.
The English duo of Ian Poulter and Paul Casey shot 67 for sole possession of fifth place at 21-under 267. Mike Weir and Ian Leggatt of Canada tied for sixth with the Spanish team of Sergio Garcia and Miguel Angel Jimenez at 268.
The World Cup was the fourth event in this year's World Golf Championships.
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