Deputy President Kgalema Motlanthe yesterday hailed "a new chapter in the story of the Muslim community in South Africa".
"This will enable the legal official recognition of the unions of Muslim couples," he said at a ceremony in Cape Town.
Imams had previously presided over weddings that were not fully recognised in civil law.
Motlanthe said Muslim couples would now have the "protective instruments" of the secular state, while maintaining "Koranic values"
Cape Town-based legal aid group, the Women's Legal Centre, welcomed the registration of the clergy as a "step in the right direction."
"It is suspiciously expedient that the government has also taken this step to apparently recognise Muslim marriages a week before an election, when it had dragged its feet on the issue for the past 20 years," said the groups' spokeswoman Magboeba Davids.
Muslims in South Africa account for just under two percent of the 52.9 million population.