The move follows a police operation that uncovered hundreds of undocumented migrants.
Many unemployed South Africans accuse foreigners of taking their jobs in a country where the unemployment rate is 24%.
Mozambique’s government said it was surprised by the deportations.
“We expected to hold talks with the South Africans to discuss the problem, but we just saw people being arrested,” said Foreign Minister Oldemiro Baloi.
A wave of xenophobic attacks in April left at least seven people dead, including one Mozambican.
Mobs targeted workers from Zimbabwe, Nigeria, Mozambique and other African countries.
Correspondents say that although South African authorities condemned the violence, they have also sought to address complaints about foreigners working illegally in the country.
Officials have strongly denied that the police operation targeted foreigners.
A government statement on Sunday said that more than 3,900 people, including 1,650 illegal immigrants, had been arrested since April’s clashes.
“We are satisfied that we have stabilised the situation and further loss of life has been prevented,” the statement said.
“Security agencies continue to work around the clock to protect both foreign nationals and South African citizens against any attacks.”
Many of the deported Mozambicans have been housed in tents in a transit centre near the capital Maputo.
When violence erupted, Mozambique set up border camps to cope with the exodus of its citizens.
Jose Macuacua said he had entered South Africa illegally and had lived there for two years selling mobile phone SIM cards.
“The police first asked for my ID, which I didn’t have,” he said, adding that he hadn’t been allowed to gather his belongings before he was taken to a repatriation centre.
Maria da Gloria Mathe said she and her husband had lived in the city of Rustenburg for four years selling clothes.
“We collected what we could in a hurry because the police were standing at the door of our shop,” she said.
South African President Jacob Zuma described last month’s violence as “shocking” and appealed for calm.
Zulu King Goodwill Zwelithini was accused of fuelling the attacks by saying that foreigners should “go back to their countries”. However, he said his comments had been distorted.