It was only the eighth time Oracle had taken the massive catamaran - the class of yacht to be used for the Louis Vuitton challengers regatta and America's Cup - on to water for training since it was launched in August.
The official website said the boat was still upside down, having floated under the iconic Golden Gate Bridge, with its wing (mast and rigid sail) "damaged nearly beyond recognition".
None of the crew were hurt in the capsize, but the team were having trouble getting the catamaran back to base.
Tactician Tom Slingsby said the boat had been preparing to bear away (turn away from the wind) when it capsized stern over bow (pitchpoled).
"We didn't know what was going to happen with the new boat," Slingsby told Oracle. "When the nose went down, the wing hit and a few guys went in the water. We were unsure if the wing would snap, so we all climbed off the boat.
"Luckily, everyone is accounted for and no one was hurt. The wing is pretty badly damaged, and we are working to get the boat back in position to return to (the team base at) Pier 80."
Local television station NBC Bay Area reported on its website that the yacht had first capsized, then flipped upside down and had begun breaking up.
The wing of the AC72 catamaran is about 40 metres tall and helps generate tremendous speed.
Challengers Team New Zealand have said their boat can reach speeds at almost twice the speed of the prevailing wind while video has shown the boat can lift its hulls totally out of the water and race on its foils.
The challengers regatta begins on July 4, 2013 and runs until September 1 before Oracle will face the winner of that regatta for the America's Cup from September 7-23.
- Tom Slingsby