A Somali man allegedly shot dead the two men, believed to be Zimbabwean nationals, outside his shop on Sunday, Lt-Col Lungelo Dlamini said.
Circumstances surrounding the shooting were unclear. The man was arrested and charged with murder and is set to appear in the Pretoria Magistrate's Court on Tuesday.
Local residents gathered in front of the shop afterwards and threw stones and looted the business. Police dispersed the crowd, but other shops were then looted.
Nine people were arrested on Sunday night and are also to appear in the Pretoria Magistrate's Court on Tuesday. Dlamini confirmed that a further thirty-eight suspects were arrested for public violence, four for possession of unlicensed firearms, and three for housebreaking and theft on Tuesday.
The thirty-eight suspects are expected to appear in the Pretoria Magistrate's Court on Wednesday.
"At this stage it cannot be confirmed how many shops were looted. It will be established as the investigation continues," Dlamini said.
"Several shop owners voluntarily removed their goods and they left them [the shops] locked."
Police monitored the area on Sunday night and no further trouble was reported.
"[On Monday] there were several people who gathered at the scene where the shooting occurred, but it is believed that most of them were onlookers, since there was strong media presence," Dlamini said.
"The area where the incident took place is a semi-informal settlement and it is believed that it is populated by both foreign nationals and the local community."
Dlamini said that more arrests could be expected as operations continued. – Sapa