Vets and volunteers from Four Paws International animal welfare group transported some 40 animals into Israel from the zoo in the southern town of Rafah. The animals - including five lions, five monkeys, four ostriches, three peacocks, two wolves, a hyena, foxes, porcupines and 10 squirrels - will be resettled in sanctuaries in Jordan and South Africa.
"The zoo has been in a bad situation in recent years due to economic and political turmoil," said Amir Khalil, a veterinarian from the Vienna-based organization. "Most of the animals had a sort of traumatization."
Many of the animals were smuggled into Gaza via tunnels beneath the southern border with Egypt, which along with Israel has blockaded the territory since the Hamas militant group seized power there in 2007, and has continued launching rocket attacks on Israeli territory ever since.
Animals kept in captivity have suffered from a combination of neglect and lack of resources on the part of zookeepers.
Some died of cold and hunger in makeshift zoos as keepers failed to provide adequate care, while others were killed during the 50-day war in 2014.
Uri Madar, agriculture coordinator for the Israeli body responsible for the crossings with the Gaza Strip, said COGAT "sees this evacuation as a mission of ethics, and will continue working in support of animal welfare in the Gaza Strip."
In January, four lion cubs died in the Rafah zoo. The owner later released grisly footage showing a lioness being declawed, in an apparent effort to push the organization to speed up the evacuation process. The owner was compensated for the animals, but the amount paid has not been publicized. There are no animals left at the zoo following the evacuation.
Four Paws International has carried out four rescue operations and has sent numerous medical missions to treat animals and birds in Gaza. Two other zoos have closed since Four Paws removed their animals, while animals are still being held in poor conditions at three other zoos.
The latest evacuation was scheduled last month, but a round of cross-border violence between Israel and Gaza militants forced the organization postpone it.
Reuters contributed to this report