The deceased, Abdikadir Isse Abdullahi, was reportedly attacked by three armed gangs who entered the shop and later shot him several times.
South African police who arrived at the scene of the incident sealed of the area and launched search operation around the area. No arrests were so far made.
Abdullahi becomes the seventh Somali national killed in South Africa in a week time. He also becomes the first Somali person to be killed in this black township, according Ahmed Rashid who also owns a shop in the area.
An Ethiopian national was earlier this month gunned down in the area by armed South African gangs, he adds.
Somalis in the country have been targeted by armed locals who loot their property while sometimes shooting shop-owners inside Black South African townships.
The rise in human rights abuse and theft cases against Somali nationals are due to the fact that Somali businessmen keep their cash in shops with poor security measures, according to a report released by South African police few months ago.
The report also says that Somali shops are located far away from major cities which make them vulnerable to attacks and robbery.
Many thousands of Somalis fled famine and warfare at home, braving a treacherous journey across the continent to reach South Africa, with most of the Somali population in South Africa living in the Eastern and Western Cape provinces.
The Department of Home Affairs, in charge of registering refugees and asylum seekers has earlier last year revealed that there were more than 32,000 documented Somalis living in South Africa, according to the BBC.
The United Nations High Commissioner for Refugees (UNHCR) also confirmed that Somali nationals were the second largest group of asylum seekers in South Africa – after Zimbabweans.
Many Somalis own spaza shops – makeshift kiosks usually run from private houses or a shack of corrugated iron. But due poverty and high unemployment in South Africa, foreigners including Somalis are prone to attacks and shops are looted or burned down as a result.
In 2008, South Africa saw a wave of xenophobic violence which saw foreigners mainly Somalis necklaced – set alight with petrol doused tyres around their necks – and their shops were burned down.
Just last March, a court in Rustenburg city has sent a South African national to 73 years in jail for killing a Somali businessman.
In passing the verdict, the court judge said the defendant was found guilty following a corroboration of evidences brought forward before the court by the plaintiff prosecution.
Pretoria recently announced that it was considering opening its embassy in Mogadishu after 20 years of absence, a move welcomed by Somali community members in South Africa.
They said that the proposed diplomatic missions in Pretoria and Mogadishu will strengthen relations between local South African and Somalis living in the country as refugees.
Somalia’s Prime Minister Abdiweli Mohamed Ali was also recently quoted as saying that his country will have its embassy in Pretoria.
The forum comes few days after a similar forum was held in Cape Town, discussing challenges faced by Somali refugees in the country.
The forum which was organised by the UN’s refugee agency was attended by heads of human right activist organizations and the Somali community in South Africa.
The meeting addressed problems faced by Somali refugees and measures needed to protect them from human rights abuses.