The swap was one of seven colonial-era name changes announced this week by Nathi Mthethwa, South Africa's arts and culture minister.
Uitenhage, a town not far from Port Elizabeth, is now Kariega. MaClear Town has become Nqanqarhu, and King William's Town is now Qonce, another name requiring mastery of a Xhosa click. There are dozens of different click sounds in the language.
One of the new names that might be easier for non-Xhosa speakers to pronounce is the one for Gqeberha's airport, which has been renamed after David Stuurman, a chieftain of the Khoi people who fought against British and Dutch colonials in the early 19th century.
Stuurman was one of the first people to be jailed on the infamous Robben Island off Cape Town. He escaped several times before he was transported to Australia on a life sentence. He died there in 1830.
Port Elizabeth was founded by British colonists in 1820, and is the largest city in the eastern cape province.
Xhosa, the language of Nelson Mandela, is spoken by about one-seventh of the population. South Africa has 12 official languages.
The renaming campaign is part of a programme to use indigenous place names in an effort to restore dignity stripped from black people during the long colonial and apartheid eras.
The new names in the Eastern Cape province were first submitted to the state's geographical committee five years ago and have been subject to intense public debate.
Denver Webb, a historian at Nelson Mandela University, in a recent paper criticised the slow pace of change and called on South Africans to "embrace name changes and come together to arrive at a set of names that reflects our diversity and that supports our constitutional principles".
Not everyone is happy about the change, however.
Several thousands of people have signed petitions opposing the city's new name, complaining that many, including non-Xhosa black South Africans, may struggle to say it.
"I have no problem in changing postcolonial names, but only those who speak Xhosa, and can do the click sound, will know how to pronounce it," said Max du Preez, the editor of Afrikaans digital newspaper Vrye Weekblad.
There have been several name changes since South Africa's first democratic elections in 1994.
The national capital is officially Tshwane, but many still say Pretoria. South Africa's main port, Durban, is officially eThekwini Metropolitan Municipality.
