Protesters "blocked the road and threw stones at the police", said Lungelo Dlamini.
"Police fired rubber bullets and then the crowd dispersed," he added.
Anger flared for a second time this week in Diepsloot township northwest of Johannesburg following riots Tuesday when a resident discovered the bodies of the girls, aged two and three, in a communal toilet.
The girls, who were cousins, were raped and strangled.
"Charges against them will be kidnapping, rape, and murder," he added.
The suspects, all men aged between 29 and 47, lived in Diepsloot.
Following the latest arrest residents hurled rocks at passing cars and shouted, according to an AFP photographer.
Some carried placards with a police sketch of one of the suspects, others with the wording "Save our children".
Located along one of the country's wealthiest gated estates, Diepsloot testifies to the country's huge wealth inequality.
Large parts of the densely-populated slum have no running water and residents share pit latrines and mobile toilets.
Over half the 54,000 crimes against children reported in the period from 2010 to 2011 were sexual offences, according to the UN children's organisation UNICEF.
Most murders occur in densely populated and poverty stricken areas with poor policing.
In a separate case, a mother was due in court today after her two young children were found dead in a field east of Johannesburg.
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