H&M had used a black child to model a sweatshirt with the slogan "coolest monkey in the jungle".
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.
The ad sparked widespread criticism, with Canadian singer The Weekend among those to voice his outrage.
"I'm deeply offended and will not be working with [H&M] anymore", he tweeted.
Police officers were on standby at the Kolonnade Mall in Pretoria on Saturday, as members of the opposition Economic Freedom Fighters (EFF) went on rampage targeting and trashing the H&M clothing store.
"Menlyn Park shopping centre management confirms protest action at our H&M store, today 13 January 2018", said Ndebele in a statement.
Meanwhile, the H&M store at the V&A Waterfront has been shut down temporarily by the Gauteng police.
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The wave of the mass store invasions, which had clearly been well organised in advance, began shortly after the stores opened for Saturday trading, with pictures and videos of the chaos lit up social media.
National Basketball Association star LeBron James, rapper Diddy and singer The Weeknd are among the celebrities who expressed shock in recent days over the H&M image, which has been removed from online promotions but continues to be circulated on social media.
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.
The firm's spokesperson, Amelia-May Woudstra, said the company was sorry for the ad, "We sincerely apologize for offending customers with an image of a printed hooded top that was published on selected global online channels".
"We will now be doing everything we possibly can to prevent this from happening again in future. We stress that our store staff had nothing to do with our poorly judged product and image".
In a series of scathing Facebook posts, she wrote: "Am the mum and this is one of hundreds of outfits my son has modelled. stop crying wolf all the time, unnecessary issue here. get over it".