Photos posted on Facebook - and which quickly spread to other social media outlets - appear at first glance to show a black doll priced cheaper than a white doll.
This prompted critics to accuse the supermarket chain, one of the biggest in southern Africa, of deeming a black doll inferior to a white doll.
In its response, Shoprite said the black and white Cutie Baby dolls were displayed next to  a bear and that the bear's price tag was mistakenly displayed underneath the black doll, prompting the outcry.
It pointed out that the label under the black doll clearly refers to the bear.
"The fact of the matter is that in Shoprite Maun in Botswana the price card of R99.95 for a plush bear was moved to underneath the Cutie Baby black doll displayed next to it. Its cost is R149.95, exactly the same as the white counterpart."
Shoprite said a picture of the incorrect display was taken and posted with a racial interpretation on Shoprite SA's Facebook wall.
"Shoprite immediately acknowledged the display error and corrected it.
"The mistake was recognised by many on social media but others took the opportunity to turn it into a racial matter and spreading the sentiment [linking] 'a price tag to colour'.
"The Shoprite Group dissociates itself from any racial or political views, preferring to continue to serve the 72% of South Africans that frequent their stores daily with the lowest prices for all," the statement said.