A worldwide media firestorm started earlier this week after pictures emerged of a young black boy model wearing "smartest monkey in the jungle hoodie".
According to South Africa's daily news24, police engaged the protesters who did not want to be caught on camera.
The ad sparked widespread criticism, with Canadian singer The Weekend among those to voice his outrage.
Protesters from the left-wing Economic Freedom Fighters (EFF) group targeted six shops in Gauteng province, police said.
In one video, claimed to have been taken at the Menlyn Park store, one of red shirted activists is seen trashing displays, kicking over and pulling down clothes rails as well as pushing over mannequins.
"Menlyn Park shopping centre management confirms protest action at our H&M store, today 13 January 2018", said Ndebele in a statement.More news: Johnson & Johnson (NYSE:JNJ) Getting Somewhat Favorable Media Coverage, Accern Reports
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H&M stores in other areas are reported to have been closed, and police are monitoring the situation.
The image advertising the £7.99 jumper was removed from H&M's United States and United Kingdom websites shortly after the outrage broke and the retailer quickly issued a statement apologising to "anyone it may have offended".
In an apology on its local website, H&M said: "Our position is simple: we have got this wrong and we are deeply sorry".
"We have a responsibility to be aware of and attuned to all racial and cultural sensitivities - and we have not lived up to this responsibility this time".
H&M also took to Instagram to express further apology, saying: 'We understand that many people are upset about the image of the children's hoodie.
"Therefore, we've not only removed the image from our channels, but also the garment from our product offering". It also promised to open an investigation and vowed that such an incident will never happen again.