South Africa's Equality Court fined Jon Qwelane $14,450 (Â£8,920) and ordered him to apologise for promoting hatred in the column published in 2008.
Headlined "Call me names but gay is NOT OKAY", it caused an uproar at the time.
Mr Qwelane, who was appointed last year to Uganda where homosexual acts are illegal, did not mount a defence.
Correspondents say the outcome of the case is particularly significant in the light of the recent attacks and rapes of lesbian women in South Africa.
Unlike in many African countries, homosexual acts are legal in South Africa and discrimination based on sexual orientation is banned, but activists say gay and lesbian people are often attacked in townships.
"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," said Vincent Moaga, spokesman for the South African Human Rights Commission, which initiated the complaint against Mr Qwelane.
The Sunday Sun officially apologised for the column following complaints after its publication, but Mr Qwelane refused to make an apology.
The court agreed with commission's argument that Mr Qwelane's article, and the cartoon accompanying it, had promoted hatred against homosexuals, causing them emotional suffering.
Mr Moaga said the money from the fine would be donated to gay rights organisations.
The BBC's Pumza Fihlani in Johannesburg says Mr Qwelane was appointed as ambassador last year, raising concerns that he would fuel tensions in Uganda which has come under intense international pressure over plans to tighten laws against homosexuality.
The Anti-Homosexuality Bill, first introduced in 2009 and yet to be voted on in Uganda's parliament, seeks to increase the penalties for homosexual acts from 14 years in prison to life.
It also proposes the death penalty for a new offence of "aggravated homosexuality" - defined as when one of the participants is a minor, HIV-positive, disabled or a "serial offender".

In recent weeks, North Korea has carried out a hydrogen bomb test and repeatedly test-fired missiles.
Mr Obama met Chinese President Xi Jinping on the sidelines of a nuclear summit in Washington on Thursday.
But hours later, South Korea's Yonhap news agency said the North appeared to have test-fired another missile.
The latest test saw what appeared to be a ballistic missile land off the east coast of the Korean peninsula, Yonhap reported.
Mr Obama said he and Mr Xi were seeking to agree "how we can discourage action like nuclear missile tests that escalate tensions and violate international obligations".
Mr Xi, quoted by China's state news agency Xinhua, said it was critical all parties "fully and strictly" implemented newly-agreed sanctions. China is North Korea's closest ally and largest trading partner.
Zheng Zeguang, China's assistant foreign minister, said the presidents had a "candid and in-depth exchange of views on a variety of issues...and reached an important consensus". He called the meeting "positive, constructive and fruitful".
North Korea's nuclear test on 6 January and a satellite launch on 7 February were violations of existing UN sanctions.
Since then, the UN and Washington passed further sanctions on Pyongyang. The UN steps were drafted with support by China and reportedly came after two months of negotiations between Beijing and Washington.
Previous UN sanctions imposed after North Korean tests in 2006, 2009 and 2013 did little to dispel its nuclear ambitions.
Much of the burden of making sure the sanctions are implemented is falling on China.
Under the new measures, any North Korean ships arriving in China must be inspected for contraband and imports halted if there is proof profits from those exchanges go towards the North's nuclear programme.
Washington has long pushed for Beijing to put more pressure on North Korea. A White House statement in February said China's "unique influence over the North Korean regime" gave it the chance to do so.
China's foreign ministry last week said it was keen to push for wider talks on North Korea, involving a number of regional powers, during the meeting with Mr Obama. There was no confirmation whether new talks were agreed on Thursday.
Mr Obama also vowed to closely work on the same issue with its allies South Korea and Japan after meeting their leaders on Thursday.
"We are united in our efforts to deter and defend against North Korean provocations," he said.
The South African ambassador to Uganda, a former columnist for South Africa's Sunday Sun paper, has been found guilty of hate speech for an anti-gay article.
[NEXT_CONCEPT]
China and the United States will work together to try to prevent further missile tests by North Korea, US President Barack Obama says.