'It wasn't easier than the first time,' said Goosen, who became the 21st multiple champion of the U.S. Open. 'Obviously, this time I knew I could do it.'
Phil Mickelson came close to winning the U.S. Open once more, but a three-putt double bogey at the par-3 17th left him with his third runner-up finish at the event after a round of 71 left him at 2-under-par 278.
'I'm not disappointed in the way I played at all,' said Mickelson. 'I just would have liked to have won, that's all. But I can't worry about the fact that somebody played better than me, because Retief played some great golf.'
Goosen was steady in the wind on Saturday with a 69, and as the course dried up, leaving unbelievably slick greens and difficult playing conditions, he put together another major championship caliber round to secure the title.
The South African, who was struck by lightning as a youngster, remains, along with fellow countryman Ernie Els, the only international players to capture the U.S. Open since 1981 when Australia's David Graham won at Merion.
Goosen buckled, but never surrendered his lead en route to his fourth career victory on the PGA Tour. He seemed poised to take the tournament by force after landing his second shot to the par-4 first in the middle of the green and quickly draining the long birdie putt to jump to 6 under.
'I wasn't letting my guard down,' he said. 'Just trying to stay focused.'
Shinnecock, which bared all its teeth over the weekend, soon caught up with Goosen, making a 6-foot putt for par seem an impossibility at the par-3 second after his tee shot found a greenside bunker.
Goosen maintained the lead at minus-5, but found trouble again with a bogey at the eighth. He had a birdie chance at the 10th, but his putt rolled 9 feet past the hole and Goosen could not make par coming back.
Things changed for Goosen at the par-3 11th, however. He hit a spectacular tee shot to four feet and converted the short birdie try to hold a two-shot lead over Mickelson. Goosen was in a world of trouble at the par-4 14th, but his putter was on fire on the back nine and he rolled in a 13-foot putt to save bogey.
Mickelson, with the support of the thousands of fans at Shinnecock carrying him from hole to hole on the back nine, made a valiant effort down the stretch and knocked his approach to 6 feet for a birdie at the 15th to join Goosen in the lead at the minus-3.
The left-hander then got some revenge at the par-5 16th, a hole that haunted him when he tied for fourth at the 1995 U.S. Open at Shinnecock. Mickelson hit his drive in the rough and advanced his second shot down the fairway. He then played his third to 5 feet and ran home the putt to take the lead at 4 under.
'I knew Phil was coming at me,' said Goosen. 'And I knew it was coming down to me and him.'
With the 16th out of the way, Mickelson soon met with a new nemesis at Shinnecock. He found a bunker off the tee at the par-3 17th and hit out of the sand to 5 feet. Mickelson could not save par, and the quick greens dragged his ball away from the hole. He had a 4-footer for bogey but again was unable to convert.
'The putt was downwind,' said Mickelson. 'When the wind gets a hold of it on these greens, it takes it. It just wouldn't stop.'
After disaster struck for Mickelson, Goosen stared down the 16th and left his third shot inside 10 feet. Just as he had been doing leading up to the putt, Goosen converted for birdie to regain a two-shot advantage.
Carefully planning his approach to the 18th, Goosen safely landed his ball on the putting surface. Unwilling to repeat his putting on the 72nd hole of the 2001 U.S. Open at Southern Hills, Goosen two-putted for par and the win.
'I didn't want to three-putt,' said Goosen, who only needed 24 putts to get around Shinnecock in the final round. 'Two-putt, win this thing, and go home.'
For Mickelson, who was trying to become the first person since Tiger Woods in 2002 to win the Masters and the U.S. Open in the same year, the end was bittersweet. He had a piece of the 36-hole lead, but gave way to the winds on Saturday. On Sunday, Mickelson fought hard in a losing effort.
He dropped a shot early at the third after a poor drive but kept his composure and ran home a 14-foot putt for a birdie at the fourth. Mickelson's second shot to the par-4 10th carried through the green on his way to another bogey, and Mickelson fell further back with a bogey at the 12th after a short putt failed to fall.
Mickelson countered again, and sank a 9-foot putt for a birdie at the 13th. A few holes later he was back in the lead at the U.S. Open, only to fall victim to the tough Shinnecock green at the 17th.
Jeff Maggert, who tied for fourth at Shinnecock in 1995, posted a 72 to finish alone in third place at 1-over-par 281. Mike Weir and Shigeki Maruyama, who held a piece of the lead after each of the first two rounds, were one shot further back at 2-over-par 282.
Fred Funk, who played alongside Mickelson in the final round, carded a 77 to take sixth place at 5-over-par 285. Robert Allenby, who began the day in a tie for 34th, shot a 70 to share seventh place with Steve Flesch at 7-over-par 286.
Jay Haas, who held a share of the opening round lead with Maruyama and Angel Cabrera, finished at 7-over-par 287 along with Els, Chris DiMarco and Stephen Ames.
Two-time U.S. Open champion Tiger Woods also struggled with the conditions on Sunday. He began the day at 4 over par and after a couple of good par saves, Woods hit a bad drive at the par-4 third and left his approach short of the green.
Woods played his third to 6 feet and failed to save par to fall back to plus-5. That was just the beginning of Woods' problems in the final round.
He dropped another shot at the eighth and followed that up with a double bogey at the par-4 ninth. Woods then bogeyed the 10th and dropped further shots with bogeys at the 13th and 15th.
The 28-year-old closed with his only birdie of the day at the par-4 18th to complete his eighth consecutive major without a win.
'I feel alright, not really great,' said Woods, whose last major title came at the 2002 U.S. Open at Bethpage. 'Actually I would like to do a little better than I am.'
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