The vaccinations were carried out in February after an outbreak among gorillas at the zoo.
Several great apes at San Diego Zoo have been given an experimental Covid-19 vaccine designed for animals after an outbreak among gorillas there.
Four orangutans and five bonobos each had two doses of a jab made by Zoetis, a veterinary pharmaceutical firm.
Eight gorillas at the zoo became the first great apes in the world to test positive for Covid-19 in January. They are now recovering.
Conservationists are concerned about the threat of Covid-19 to great apes.
They are particularly worried about the danger to gorillas, which have populations that are listed as critically endangered on the IUCN Red List.
“This isn’t the norm,” Nadine Lamberski, chief conservation officer at the San Diego Zoo Wildlife Alliance, told National Geographic.
“In my career, I haven’t had access to an experimental vaccine this early in the process and haven’t had such an overwhelming desire to want to use one,”
Karen, the first orangutan in the world to have open-heart surgery in 1994, was among those to get a jab.
Ms Lamberski said the apes had not suffered any adverse reactions and would soon be tested for antibodies to determine if the shots were a success.
Cases of the virus have also been found in animals at other zoos, including lions and tigers in the Bronx Zoo in New York, and lions at Barcelona Zoo in Spain.
Covid-19 infections have been confirmed in various animals worldwide, from dogs and cats to ferrets and mink. However, cases are generally quite rare.
Zoetis started developing a Covid-19 vaccine for cats and dogs in February last year after a dog tested positive for the virus in Hong Kong.
The vaccine was deemed safe and effective in cats and dogs by October last year.
Until February this year, the jab had not been tested on any other animals.
But Ms Lamberski told National Geographic that vaccinating the zoo’s great apes was worth the risk.
“We commonly use vaccines designed with dogs and cats for lions and tigers,” Ms Lamberski said.