“As part of easing tensions and [to] heal the community… people from all religious background will engage in prayer and meditation,” spokesman Nkosinathi Nkabinde said in a statement.
The prayer session would form part of the international 16 Days of Activism Campaign, from November 15 to December 10.
Three children have been killed in the township since September.
The bodies of two-year-old Yonelisa Mali and her cousin Zandile Mali, three, were recently found in a public toilet cubicle.
Five people were arrested, but four of them were released due to lack of evidence.
The prayer day would include a march led by Gauteng premier Nomvula Mokonyane and Johannesburg mayor Parks Tau. Church leaders would also be present.
“The community will be addressed on various issues about crime, substance abuse, domestic violence and gender-based violence,” said Nkabinde.
The prayer day would take place on Monday at the Diepsloot Methodist Church, in extension 10.