Two of the fires occurred on Saturday evening and one in the early hours of Sunday morning, they said.
"An adult male and female sustained fatal burn wounds and were declared deceased by medics" at one of the informal settlements, the Cape Town's fire and rescue spokesman Jermaine Carelse said in a statement.
The biggest fire which happened around 2:30 am on Sunday engulfed over 150 shacks leaving over 1,000 people displaced in the Mfuleni settlement, some 30 kilometers (19 miles) southeast of Cape Town.
The cause of the fire is under investigation, Carelse said.
Shack fires are common in South Africa and are a perennial threat to the impoverished residents of the sprawling informal settlements near major cities throughout the country.
According to the housing ministry as of 2022, 12.3 percent of people lived in shacks in South Africa.
Thirty years after the end of apartheid, land ownership and housing policy are still hotly disputed issues in the country's politics and a key talking point in the upcoming May 29 polls.
South African Muslim charity Gift of the Givers told AFP it was bringing humanitarian aid to the homeless at all three locations, including hot meals and clean drinking water as well as blankets, mattresses and baby care products.
A handful of people were being treated for injuries, while one remained missing, the charity said, adding that community halls were being organised to house the displaced.