The Thelle Mogoerane hospital in the eastern Johannesburg township of Vosloorus has been in the grip of the antibiotic resistant bacteria since July 11.
"We can no longer admit babies here," said Health Minister Aaron Motsoaledi in a media briefing on Sunday.
Another case of Congo virus reported in city
The affected patients are being transferred to another government hospital as well as the Nelson Mandela Children's Hospital, which opened in Johannesburg 18 months ago, he added.
The health minister said overcrowding undermined the facility's infection control measures.
He said neonatal wards in Gauteng province, which includes the financial hub Johannesburg and the capital Pretoria, were at 132 percent capacity on average.
The province has huge numbers of patients from neighbouring countries including Zimbabwe who travel to South Africa in search of better quality care.
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