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The 65-year-old software tycoon was on-board his incredibly fast craft on Sunday, after sitting out Race 1 due to a weight limit.
Ellison's victory over rival billionaire Ernesto Bertarelli sends the oldest trophy in international sports to San Francisco's Golden Gate Yacht Club.
The two billionaires have been locked in a tumultuous legal fight for 2½ years, and it looked for a while like the result of this race was going to be contested off the water.
Alinghi raised a red protest flag on its giant catamaran late on the first leg of the triangle course, leaving everyone wondering what it was about since there's no communications off the boats.
The Swiss dropped the protest after the race, confirming Ellison's win.
"It's absolutely an awesome feeling," said Ellison, the CEO of Oracle Corp. "I'm very proud to be a part of this team."
The America's Cup has been away from US shores for 15 years, the longest drought since America won the silver trophy by beating a fleet of British ships around the Isle of Wight in 1851.
Dennis Conner lost it in 1995 to Team New Zealand and Russell Coutts, a three-time America's Cup winner who is CEO of BMW Oracle Racing.
Besides Ellison, tactician John Kostecki was the only other American on BMW Oracle's crew. It was steered by skipper Jimmy Spithill of Australia, who at 30 is sailing in his fourth America's Cup.
"The boys are just absolutely lit up," Spithill said. "Larry's stoked, Russell's stoked and we just can't wait to get back to shore to celebrate."
While Ellison's fortune made the victory possible, the true star was his monster black-and-white trimaran and its radical 223-foot wing sail, which powered the craft at three times the speed of the wind, sending its windward and middle hulls flying well above the water.
When the yacht hooks into a breeze, it seems as if Spithill is jamming down an accelerator.
One of the lasting images of this Cup will be that of Spithill, decked out in technology seemingly straight out Star Wars, calmly steering the boat from his airborne helm.
"It's just such an awesome tool for racing," Spithill said.
The American trimaran took a 28-second lead rounding the first mark and then accelerated over the Mediterranean while sailing across the wind on the second leg, its windward and middle hulls flying out of the water.
These were the fastest, most technologically advanced boats built in the 159-year history of the America's Cup.
The final margin was 5 minutes, 26 seconds. Alinghi had to do a 270-degree at the finish, the result of its second prestart blunder in as many races.
BMW Oracle seemed to get an instant boost when Alinghi was penalized for being in the starting box before the 5-minute gun sounded. While the Americans headed out to the left side of the court, Alinghi did a downspeed tack and took the right side.
The move paid off when the Swiss gained during a wind shift and powered into the lead about a third of the way up the leg. Multihull whiz Loick Peyron of France took Alinghi's helm from Bertarelli early in the leg.
Alinghi crossed ahead of BMW Oracle approaching the first mark, but lost speed during a tack and the Americans sailed ahead.
Ellison, a self-made billionaire, joins Harold Vanderbilt, Ted Turner and Bill Koch among the tycoons who've hoisted the silver trophy.
He's got a ways to go to catch Conner, though. Conner won the America's Cup four times and lost it twice. Conner's victory in 1987 in Fremantle, Australia, was a bit more stirring, as he went Down Under with determination to reclaim the Cup he'd lost four years earlier, ending the New York Yacht Club's 132-year winning streak.
Ellison's victory ended one of the most bitter chapters in the 159-year history of the America's Cup, which has often been a clash of egos as well as boats.
He and Bertarelli fought over their interpretations of the 1887 Deed of Gift, which governs the America's Cup. Ellison's syndicate eventually prevailed, forcing this rare head-to-head showdown.
This was only the second Deed of Gift match in modern times. The other was in 1988, when Conner steered his catamaran to a two-race sweep of New Zealand's big monohull in San Diego.
The America's Cup should return to its normal system of several challengers competing in sloops for the right to face the defender.
The ornate trophy itself is headed for the Golden Gate Yacht Club, which sits on a public jetty in the heart of San Francisco's cityfront, with views of one of the world's most famous bridges and Alcatraz Island.