The Western Cape provincial government condemned the two "despicable" attacks on mosques in Kalk Bay and Simonstown since Saturday.
"Both incidents made calculated use of Islamophobic methods," it said in a statement.
"The similarity of the cases, and proximity of the mosques, raises concerns that the two incidents may be linked."
South Africa has a history of relative religious tolerance, and Western Cape premier Helen Zille said that "acts of religious or racial prejudice have no place in our province and nation."
Achmat Sity, imam of Masjidul Jamiah in Kalk Bay, told AFP that the caretaker at the mosque -- which is more than 110 years old -- had discovered the vandalism last morning.
The provincial branch of the ruling ANC party condemned the attacks as "disgusting" and called on South Africans "to stand united in protecting the culture of coexistence."
About 1.5 per cent of South Africa's population is Muslim.