Goals from Dirkie Chamberlain, Sulette Damons and Jade Mayne repelled the Belgians, who scored the opening goal after 22 minutes.
Belgium pulled one back after trailing 3-1, but the South Africans held on for the win.
South Africa lead the six-Test series 1-0 after the first Test was drawn 1-1 and the second Test 2-2.
The fourth Test takes place on Thursday.
Source: Sapa