Images of the charred mosque, located in the suburb of Effingham, showed forensics officers on site and community members inspecting the damage.
"The attack happened in the early hours of the morning at around 1:30 a.m. (2330 GMT)," Islamic elder Mohammed Tariq told AFP, adding that no-one was injured because of the early hour.
"The mosque itself has been burnt extremely badly and emergency personnel have been on the scene. A case of arson has been opened," he said. Police could not be reached for comment.
The attack comes amid tensions between Muslim factions in South Africa, a country that prides itself on its religious tolerance.
They allegedly stabbed worshippers at the mosque near Durban. Police said the attackers' motive was unknown but "elements of extremism" were involved.
At the time one Muslim leader said the mosque was targeted because it was a Shia place of worship that had received previous threats, exposing deep tensions between the Shia and Sunni population.
In June, two worshippers were stabbed and killed at a mosque in Malmesbury, 70 kilometres (45 miles) northeast of Cape Town.
In November, a 30-year-old man was shot dead and an imam was injured in an attack on a mosque in Cape Town.
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