The 20-year-old animal, named Kilwon, was kept in appalling conditions in Indonesia's largest zoo, Surabaya, in Java.
As the last living giraffe in the zoo, his death has brought new attention to the terrible plight of animals kept at the well-known tourist attraction, which once claimed to own the most impressive wild animal collection in southeast Asia.
Emaciated tigers and 180 pelicans packed so tightly in one cage that they cannot move have also been found.
According to reports in the Daily Mail, there have been persistent suspicions that members of the staff at Surabaya Zoo are also involved in illegal wildlife trafficking.
The zoo was criticised two years ago after reports emerged that 25 of its 4,000 animals were dying prematurely every month. These included an African lion and a Sumatran tiger.
The government ordered a clean-up campaign, which reduced the mortality rate, but since then conditions have deteriorated again.
Sixteen tigers are kept in a prison-like row of concrete cages, and one white tiger who has been at the zoo 20 years is covered by skin lesions and is unable to stand up properly.
Speaking to the AP, former zookeeper Ian Singleton, who runs an orangutan conservation programme in Sumatra said: "This is extremely tragic, but by no means surprising in Indonesia's zoos, given the appalling way they are managed on the whole."
Following the death of the giraffe, protesters have appeared at the zoo gates to highlight the terrible treatment of the animals.
Tim Phillips, campaigns director at Animal Defenders International, called for the closure of the zoo.
"This was a tragic, pointless and painful death of an animal living in miserable conditions," he said. "With all the natural wonders and beauty of Indonesia you have to ask why such a horrible exhibit is allowed to continue where animals live and die in miserable pens."
"Tourists and locals need to turn their back on these unnatural exhibitions, and instead enjoy the country's natural flora and fauna, and support genuine conservation projects helping animals in the wild. Establishments like this do nothing for conservation nor animal welfare and, as can be seen from recent tragic incidents, the animals are utterly vulnerable. Surabaya Zoo should be closed."
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