Meandering along the Limpopo river, the Beitbridge border between South Africa and Zimbabwe is prone to illegal crossovers, especially by economic migrants who often crawl through broken sections of the fence.
Public Works Minister Patricia de Lille announced she had invoked emergency procurement procedures to build or repair fencing on either side of the Beitbridge Border post.
"This is to ensure that no undocumented or infected persons cross into the country and vice-versa," she said as South Africa's infection numbers jumped to 150 on Thursday from 116 the previous day.
"This is in line with one of the measures announced by the president in that South Africa's borders and ports are to be secured with immediate effect," she said in a statement.
President Cyril Ramaphosa has ordered that 35 of the 53 land entry points be closed as coronavirus infections in South Africa rise rapidly.
"This measure will, however, not be effective if the fences at the border are not secure, which in many places, they are not."
Construction is due to start this week.
"All 40 kilometres of fence will be finished within one month," she said.
Fixing the 1.8 metre-high fence will cost approximately R37.2 million.
South Africa currently has the most infections in sub-Saharan Africa.
Most cases are people who recently returned from abroad, especially Europe, but the number of local infections is increasing.