Some of those trapped were lowered by firefighters using harnesses, according to reports.
Gondolas malfunctioned after a gust of wind tripped a circuit breaker on the Bayside Skyride, police in the US city told FOX5 News.
Nine adults and seven young people were trapped on five gondolas, the San Diego fire rescue department said.
The rescue, which started at about 6pm local time, came to an end just before 11pm, the BBC reported.
Among those rescued were an infant and a partially paralysed passenger who had recently suffered a stroke, according to local TV reports.
Lifeguards were also on hand in the water below during the rescue,
SeaWorld said it had been in contact with the guests via intercom during the rescue, and that blankets were available on board each gondola.
The company added it would conduct a “thorough inspection” of the ride before re-opening it.