The Border Management Authority has temporarily closed the Pafuri Border Post and Giriyondo Border Post due to flooding caused by heavy rainfall.
Authorities say rising water levels have created safety risks for travellers, prompting the precautionary shutdown of both ports of entry between South Africa and Mozambique.
Border Management Authority Commissioner Michael Masiapato confirmed that staff members and vehicles stationed at the affected crossings have been evacuated.
No injuries or damage to infrastructure have been reported at this stage.
Officials are also closely monitoring river levels in areas near the Kruger National Park as the heavy rains continue.
The Border Management Authority says operations at the affected ports of entry will resume once conditions improve and it is safe to do so.