Lee said the new James R. Herman Cruise Terminal at Pier 27 serves as part of the "reawakening of our whole waterfront."
America's Cup organizers will be the first tenants in the two-story building, which will serve as the headquarters of the races that will run for several weeks between July and September.
Following the regatta, construction will recommence to make the terminal operational for cruise ships by 2014. The site will also include a 2.5-acre public park called the Northeast Wharf Plaza, according to the mayor's office.
"These are great gifts that I think will last for many generations to come," Lee said.
The terminal at The Embarcadero and Lombard Street will be able to handle vessels carrying up to 2,600 passengers, who will get off their ship to expansive views of Coit Tower, Telegraph Hill and the city's skyline.
"From the moment of arrival, visitors will be beckoned out to the experience that is San Francisco," Port of San Francisco executive director Monique Moyer said.
During the roughly three-quarters of the year that cruise ships will not be in port, the facility will also be able for use for weddings and other private events, Moyer said.
The terminal is named after Herman, the former Port Commission president who "was adamant that San Francisco not leave behind its maritime roots," Moyer said.
She said, "Our city will always be a world-class waterfront city."
Cruise ships bring an estimated 200,000 passengers to San Francisco each year and more than $30 million to its economy, according to port officials.