Two worshippers were killed early on Thursday morning and the killer was shot dead by the police at a mosque in Malmesbury, in the Western Cape.
The motive is unknown at this stage.
The attack comes a month after a separate incident on a mosque in Verulam, KwaZulu-Natal where three unknown men stormed the place of worship, killing one person and injuring two others.
The Muslim Judicial Council (MJC) has condemned the incident.
Representatives of the MJC are currently at the residence of the deceased.
The MJC representative Moulana Abdul Khaliq-Allie said he would like to express his gratitude to the broader society who have shown them support during this tragic time.
[Thank you to] The interfaith communities for sharing at this tragic moment with the Muslim community.— Moulana Abdul Khaliq-Allie, MJC representative
He adds that even though the information is sketchy, there was a programme being held at the mosque and at the closure of the night prayer.
It is in the nature of Muslim people to be welcoming to people who want to join in prayers. And it is very traumatic, very sad and very disturbing for the local community here but for the broader South African community.— Moulana Abdul Khaliq-Allie, MJC representative
Listen below to the full interview, we apologised for the poor sound quality: