Government agency Te Whatu Ora/Health NZ asked the court in Auckland to take over guardianship of the boy, whose operation had been delayed because his parents did not want doctors to use donated blood from anyone who had the Covid-19 vaccine.
The four-month-old has a condition called pulmonary valve stenosis - a blockage in his heart. He urgently needs open heart surgery, which is likely to require a blood transfusion.
In a decision tonight, Justice Gault also said doctors from Te Whatu Ora had been made agents of the court to carry out the surgery, including the administration of any blood products.
They were instructed to keep the baby's parents "informed at all reasonable times of the nature and progress of (the baby's) condition and treatment".
His parents were agents of the court for all his other care.
A request by the family's lawyer to force the NZ Blood service to take blood from an unvaccinated donor of their choosing for the surgery was declined.
The service does not make a distinction between vaccinated and unvaccinated donors, and has said there is no extra risk posed.
Haematologist and transfusion medicine specialist Dr Jim Faed said there was no evidence of any risk associated with blood from a person who has been vaccinated against Covid-19.
Any vaccine in the blood was broken down quickly after the injection, he said.
Te Whatu Ora had applied to the court under the Care of Children Act asking that the doctors have temporary guardianship of the baby for his medical care only.
Its lawyer said in court last week that the baby could get more sick with every heartbeat, and he could deteriorate suddenly - so the case was heard urgently.
Te Whatu Ora told the court yesterday that doctors could be ready to operate within 48 hours of getting the go-ahead.
Name suppression applies to the child and family.
