Alinghi led around all marks to win by 40 seconds, taking a 2-0 lead in the five-of-nine-race challenger series.
He has coasted through the last two Cups, and in the challenger series here, he sailed conservatively to bank his speed gains.
At 3-4, Prada is the biggest surprise of the challenger series.
Under the new arrangement, a single event authority will oversee both the challenger series and the Cup finals and negotiate media rights to the event.
She had the highest point total and was the clear leader of the challenger series.
The event was part of the challenger series and was played on outdoor hard courts.
Prada, which captured the final two races of the challenger series to win it by 5-4, triumphed today by 49 seconds.
The victory gives Alinghi a 3-0 lead in the five-of-nine-race challenger series.
This means that any syndicate from the country of the defending yacht club would not be participating in the challenger series.
The event began as a Futures tournament from 2004-05 and is now part of the challenger series.