Bird conservation groups that pushed for the protection welcomed the settlement in the Pretoria High Court as a milestone in the fight to save the distinctive southern African black-and-white birds.
The order makes the waters around six key breeding colonies off limits to commercial sardine and anchovy fishing for at least a decade, according to a copy.
They include Robben Island about 10 kilometres (six miles) off Cape Town, that is most famous for its jail where Nelson Mandela was held for 18 years until 1982.
Other zones are the uninhabited Dassen Island, further up South Africa's Atlantic coast, and the Stony Point nature reserve.
"This order of court is an historic victory in the ongoing battle to save the critically endangered African Penguin from extinction in the wild," said BirdLife South Africa, one of the groups that had called for the protection.
The International Union for Conservation of Nature listed the African Penguin critically endangered in October 2024.
Conservationists say that 97 percent of the population is already lost and, at the current rate of population decrease, the bird could be extinct in the wild by 2035.
The dwindling numbers are due to a combination of factors including disturbances and oil spills, but the biggest threat is linked to their nutrition, conservationists say.
When penguins do not eat enough, preferably sardines or anchovies, they tend to abandon breeding, they say.
There were more than 15,100 breeding pairs in 2018 but this dropped to around 8,750 by the end of 2023, according to BirdLife South Africa.
Tuesday's ruling gives the environment minister two weeks to implement the closure of the six breeding sites.
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