Management of the Stellenbosch Mediclinic says strong winds have damaged the roofs of structures at the facility.
It says this has affected operations in surgical and paediatric wards.
Three neonatal patients had to be transferred to an alternative hospital.
Strong winds caused havoc across the Western Cape at the weekend.
Trees were uprooted and houses as well as schools were damaged.
The Education Department has closed schools in the Boland and the Helderberg Basin after the South African Weather Service issued a warning for inclement weather conditions.
Disruptive winds and a big shack fire in Stellenbosch have also left many people destitute.
VIDEO | Hundreds left homeless after shack fire in Kayamandi:
Calls for donations
The City of Cape Town has called on the public to help with donations for victims of the winds and fires in the metro and surrounding areas.
The City’s Disaster Risk Management Centre says donations can be channelled directly to its office in Goodwood.
Meanwhile, the humanitarian aid group, Gift of the Givers, says it will assist residents of Lwandle and Nomzamo in Strand after their dwellings took in water overnight.
The wind has subsided in some areas, but disaster teams remain on high alert.
