Two repatriation flights for US citizens departed on Thursday, with a third expected to leave on Friday.
"Together, these flights, all bound for Washington DC, will take over 900 Americans from South Africa back to the United States," US Embassy spokesperson Robert Mearkle said in a statement.
The first flight left at 14:35 from Cape Town International Airport after leaving King Shaka International Airport in KwaZulu-Natal on Thursday morning.
The second departed at 16:16 from OR Tambo International Airport, with the third expected to depart from Cape Town on Friday.
US Ambassador to South Africa Lana Marks hailed the international relations and cooperation and transport departments as well as Airports Company South Africa for their "excellent collaboration" in facilitating the departure of the US citizens.
"The Department of State has no greater priority than the safety and security of US citizens overseas. We are rising to meet the historic challenge posed by the Covid-19 pandemic and, as of today, the department has repatriated over 52 000 citizens on over 519 flights from over 98 countries," Marks said.
Last week, Transport Minister Fikile Mbalula said the repatriation of foreign nationals from South Africa was allowed, provided that chartered aircraft were manned only by a crew who would not be allowed to disembark.
International Relations Minister Naledi Pandor said the government would allow citizens stranded abroad to return to South Africa.
"All airport, airline, and US Mission personnel followed all recommended protocols for personal protection and distancing throughout the repatriation operation. Once in the United States, all passengers will need to self-quarantine for 14 days," it added.