“One baby was seven-months-old and the other was 13-months-old,” said spokesman Tebogo Lekgethwane.
The circumstances surrounding their deaths were similar to the first baby that died last Wednesday, he said.
Dozens of residents went to local clinics to be checked out last week following the contamination. Five babies were admitted to hospital for observation.
The Lekwa-Teemane municipality shut down its water supply system more than a week ago. The national water affairs department on Friday said the system had been cleaned and sanitised, and water was restored on Thursday evening.
But residents said the water coming out of taps was still brown on Friday, and residents were asked to boil the water first before using it. Water samples were taken for testing, but the outcome is not yet known.
The health department denied claims of a cholera outbreak, saying the outcome of the tests was still being awaited.
On Sunday, Water and Sanitation Minister Nomvula Mokonyane visited the area. Her spokeswoman Nomvula Khalo told Sapa she expected to receive the results on Monday afternoon.