Men’s hostels in Johannesburg housing mainly South Africans were searched for weapons and 11 arrests were made.
The army was ordered to deploy to volatile areas to stop further attacks that began about three weeks ago.
At least seven people have been killed and 5,000 have been left homeless since the xenophobic violence began.
The army was also deployed during similar violence in 2008, when at least 63 people were killed.
The first deployments were to Alexandra, a poor township north of Johannesburg, where Mozambican Emmanuel Sithole was killed at the weekend.
The hostels are communal areas still owned by the government that used to house mine labourers during the days of white-minority rule.
The BBC’s Nomsa Maseko, who witnessed one raid in Johannesburg’s Jeppestown, says they are often the target of raids when the police are looking for firearms during a crackdown on crime.
No weapons were found during the raids overnight, and it is believed there may have been a tip-off, she says.
Police say 11 arrests were made for possession of marijuana and suspected stolen items.
A helicopter hovered above one hostel in Jeppestown, as inside police moved from floor to floor conducting searches where the residents were made to lie face down in the corridors, the AFP news agency reports.
On the streets of the neighbourhood, soldiers stood in groups of about six, positioned within a few metres of each other, it says.
Troops have also been despatched to KwaZulu-Natal province, where the unrest began following remarks by Zulu King Goodwill Zwelithini.
The powerful monarch has denied fuelling the xenophobic attacks, saying at a rally on Monday: “If it were true that I said foreigners must go, this country would be up in flames.”
More than 900 people have been voluntarily repatriated to their home countries since the violence broke out, officials say.
Defence Minister Nosiviwe Mapisa-Nqakula said the troops were being sent in “as the last resort. The army will serve as a deterrent”.
With the unemployment rate at around 25%, many South Africans accuse foreign nationals of taking jobs from locals.
Official data suggests there are about two million foreign nationals in South Africa, but some estimates put the number much higher.