Nkosiyapha Kunene, 36, and his wife Virginia, 32, who admitted the manslaughter of their son Ndingeko, received three years, and two years, three months' imprisonment respectively.
Mr Justice Singh, at the Old Bailey, said: "The right to manifest one's religion is not absolute. It is limited in particular by the rights of others. The state has a particularly important duty to protect the right to life, especially when a young child is concerned."
The couple, of Erith, Kent, who the judge said were strict Seventh Day Adventists, admitted the charge at earlier hearings.
The judge said Ndingeko was born on January 1, 2012. He was found to have rickets resulting from severe Vitamin D deficiency.
The judge said the vitamin D deficiency was not diagnosed at birth. But the mother did not attend a scheduled check-up on March 8 and Ndingeko was not seen by a health care professional from then until the day he died.