According to Brazil's Globo TV and A Tarde newspaper, doctors extracted the needles that posed the greatest threat to the toddler's life - from his lung and close to his heart, reports the Telegraph.
A hospital spokesman said the boy's condition was stable after the 3-hour operation.
He added that doctors from the Salvador hospital will review the baby's progress before undertaking two more operations to remove the remaining needles.
The tot's mum, a maid, had recently brought him to the hospital saying that he was suffering from bouts of pain.
Although, the mother says she has no idea how the needled entered her son's body. The police is looking for the boy's stepfather, who allegedly inserted the needles in his body while conducting bizarre rituals.