The attack on the Imam Hussain (AS) Mosque left one person dead and three others critically wounded during the month of Ramadan.
The MJC says the Muslim community has been on edge since the incident as it seemed authorities were not making headway in their investigation.
Police Minister Bheki Cele announced the trio's arrests Friday.
The MJC's Shayk is-Gaak Taliep has urged the Muslim community to respect the rule of law and allow justice to take its course.
“We are thankful to Saps, the Hawks, the NPA and all others involved. We are confident that they will face the full might of the law.”