The gratuitous display of the old apartheid flag constitutes hate speech, the Equality Court, sitting in the Gauteng High court in Johannesburg, ruled on Wednesday.
The Nelson Mandela Foundation and Human Rights Commission took the case to court, asking that the gratuitous display of the flag be stopped.
Handing down judgment on Wednesday, Judge Phineas Mojapelo said the display of the old flag gratuitously demeans and dehumanises on the basis of race. He added that it impairs dignity.
He further said that Afriforum's defence of freedom of speech is illogical and is therefore dismissed.
Mojapelo said the order is not a banning order against the old flag.
In their application, the foundation argued that the display of the flag was a symbol of white supremacy, which was degrading and dehumanising to black people.
In a final submission before the court in April, the foundation's legal representative, advocate Tembeka Ngcukaitobi, said there were limits to freedom of speech, which should also apply to the display of the apartheid flag.
But lobby group Afriforum argued otherwise, saying although it condemned the use of the old flag, it should not be declared hate speech.
The display of the flag became a matter of concern for the foundation after it was displayed during a "Black Monday" protest organised by Afriforum in October 2017.
The lobby group was protesting against the scourge of farm murders in South Africa.