The final group of 219 Ugandans arrived at Entebbe International Airport at 11:20 p.m. on Thursday aboard a Uganda Airlines chartered flight from Johannesburg, bringing the evacuation mission to a close.
Uganda's High Commissioner to South Africa, Ambassador Paul Amoru, accompanied the returnees on the final flight and described the operation as a significant humanitarian achievement.
"I had the honour of accompanying the final flight of Phase I, carrying 219 Ugandan nationals from Johannesburg back home to Uganda," Amoru said.
"This has been an important chapter in a humanitarian mission that reunited families, restored hope and reaffirmed our government's commitment to protecting Ugandans wherever they may be."
The government said the operation evacuated Ugandans from Johannesburg, Cape Town and Durban after xenophobic unrest disrupted their lives, forcing many to seek assistance to return home.
The completion of the exercise comes a day after another Uganda Airlines charter flight brought back 153 Ugandans from Cape Town, raising the number of returnees at the time to 1,033.
That flight also transported the remains of a Ugandan national who died during the violence linked to protests targeting foreign nationals.
The Ministry of Foreign Affairs launched the voluntary repatriation programme after receiving requests for assistance from Ugandans stranded in South Africa as attacks on foreign nationals escalated in several communities.
Government said the exercise was fully funded and voluntary, targeting citizens who wished to return home because of the deteriorating security situation.
Several returnees earlier recounted fleeing their homes and businesses with little more than the clothes they were wearing after their property was looted, destroyed or abandoned during the unrest.
The recent violence in South Africa followed protests by some local groups demanding tougher enforcement of immigration laws and the removal of undocumented migrants. In several affected areas, foreign nationals became targets of attacks, looting and intimidation.
The latest evacuation concludes the first phase of Uganda's emergency response to the crisis, although authorities have not yet indicated whether a second phase will be undertaken for Ugandans who may still require assistance.