The man in an email said that, in order to obtain his residence permit, he had undergone medical test only to be informed that he was HIV+.
"The next day I was called by the human resources department of Al-Jazeera and was told to report to their office at 7:00 am the next morning. I was driven to the prison by one of the officers from Al-Jazeera and admitted into prison custody," he said.
He was then deported back to South Africa. "I have not been contacted by anyone in management from Al-Jazeera since I was deported," he said.
"I really simply want my job back, a job I can actually do from the Johannesburg offices of Al-Jazeera," he said.
A public interest legal group, Section 27 said that it asked South Africa's delegation to the International Labor Organization to file a complaint against Qatar, which barred outsiders with HIV from their nation.
The journalist whose identity was kept under wraps, was named a senior editor for Al-Jazeera's network website in Oct 2010, said the group.
"Any employee moving to a new country has to pass the immigration requirements there," said an Al-Jazeera spokesman.
"Al-Jazeera is an equal opportunities employer, but obviously cannot circumvent the national regulations governing any of its worldwide offices," the spokesman added.
Qatar is among one of the five countries which bans entry to people having HIV, a law that Section 27 said does not abide with the country's duties under international law.
The group said that since the journalist would not be allowed in the country to contend his dismissal in court, it asked South Africa to seek action at the ILO.