Pastor Mpfariseni Mukhuba was arrested and her church was ransacked by the police for noise making and breaching the Disaster Management Act.
The police were responding to complaints of noise and violation of Covid-19 regulations.
The clash between the police and the members of the United Fellowship Church in Soweto left both police officers and church goers injured.
The church members gathered in their hundreds in contravention of the Disaster Management Act. Gatherings of more than 50 people are are prohibited.
The events occurred hours before President Cyril Ramaphosa declared that South Africa was moving to lockdown level 1.
The Johannesburg Metro Police were forced to use rubber bullets to disperse the aggressive crowds. Several members of the church were also arrested.
Church goers hurled unChrist like insults in the presence of children. Pastor Mukhuba is well known in Soweto and She has been conducting her services in the area for years.
Reports are saying about 2000 people attended the church service.