Commission spokesman Vincent Moaga said a judge ruled that the 2008 newspaper column headlined "Call me names, but gay is NOT OK" by veteran journalist Jon Qwelane promoted hatred. Qwelane was ordered to apologize and pay a fine of 100,000 rand (about $14,000) that the human rights commission will donate to a gay rights organization.
Qwelane, who was in the Ugandan capital Tuesday, did not mount a defense in the case filed by the commission.
An aide at the embassy said Qwelane was meeting with a delegation from South Africa when The Associated Press called for his reaction, and he did not immediately respond to an e-mail seeking comment.
Moaga said the case sent an important message at a time when a series of rapes and other attacks on lesbians has raised concern about homophobic violence in South Africa.
"We are hoping really that this finding will send a message to community members, a message that says gay and lesbian people have an equal right to the protection of their dignity and rights," Moaga said.
Moaga said his commission takes no position on whether Qwelane, appointed last year, should continue serving as ambassador, but that he expected the government to review the court ruling.
Uganda has been criticized by international human rights groups since one of its lawmakers proposed in 2009 that gays should face the death sentence in some cases. The Ugandan parliament has yet to vote on the bill.
Same-sex marriage is legal in South Africa and the country has among the most liberal laws on sexual orientation on the continent. But the ideals expressed in the constitution at times clash with the realities of prejudice.
"One of the major legacies of apartheid is that of intolerance towards difference -- be it in terms of race, religion, nationality, ethnicity, sexual orientation or other such factors," the human rights commission, a government agency, said in a statement about the Qwelane case. "As a result, 17 years after South Africa's first democratic elections, the country is still grappling to find ways to better manage difference."