The ad in question featured a black child wearing a green hoodie with the phrase "coolest monkey in the jungle" on the front. The Weeknd ended his collaboration with them, and social media in general spurned the retailer for the offensive imagery.
Footage uploaded to social media shows protesters throwing clothing racks to the floor and kicking mannequins.
Protesters from the left-wing Economic Freedom Fighters (EFF) group targeted six shops in Gauteng province, police said.
Protestors went on the rampage inside the store earlier on Saturday and police responded with rubber bullets.
The party's leader, Julius Malema, said in a speech on Saturday that the EFF "make no apology" for their actions in trashing the stores, and that targeting them was "just the beginning". "We continue to monitor the situation closely and will open the stores as soon as the situation is safe again".
The image copped widespread criticism, with USA singer The Weekend among those to voice his distaste, saying he was "shocked and embarrassed".
She has also revealed the comments sparked a wave of online abuse and had even been called a "monkey" - the same racist slur that sparked the outrage.
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He said that Pakistan is facing serious problems from the elements carrying out attacking from Afghanistan's soil. Sharif's brother, Shahbaz, is also a potential candidate for the prime minister job.
Innocent shoppers were forced to flee as activists swept through the stores, which included Africa's flagship H&M stores in the upmarket suburb of Sandton, Johannesburg.
EFF supporters destroyed the window of the store, vandalised property and stole from it.
The company has since apologised for the advertisement.
No arrests have been made so far but police are now investigating a case of malicious damage to property.
"We strongly believe that racism and bias in any shape or form, deliberate or accidental, are simply unacceptable", the statement reads.
"We stress that our store staff had nothing to do with our poor judgement of producing the children's hoodie and the image", it added.