The court decision - which came with extensive identity suppression orders - goes beyond the voluntary agreement signed with the health board a month ago, making his son a ward of the court.
But it also incorporates the father in a shared guardianship role as the court's agent to parent the boy - on condition he allows treatment to go ahead.
The father told the court he reached his views over years researching HIV on the internet. The research came after his wife died from an unusual infection then tested positive for HIV. While the man is not HIV-positive, tests on the couple's youngest child showed the boy had picked up the virus from his mother.
The man had never accepted his wife or son had been correctly diagnosed but said, even if they were HIV-positive, the accepted forms of treatment had side effects which outweighed the benefits.
The health board - which accepts the boy's father and stepmother are "highly responsible parents" - took the case to compel treatment after tests showed the boy's resistance to an Aids-related condition was growing.
Justice Patrick Keane took the expert opinions of the clinicians over the father's views, saying there was no doubt about the boy's diagnosis or that HIV led to Aids. He also said he accepted the clinicians' evidence side effects would subside after a short period. Evidence was also given the drugs would allow the boy to live a virtually normal life.
Justice Keane said a lawyer would be appointed for the boy in November 2016 ahead of a review of the case in March 2017. If the boy had been told he was HIV-positive, his views would then be heard.
He rejected a plea for an 18-month order, saying the boy's "condition will remain unchanged until he is 16 and, indeed, for the rest of his life, as will his need for medication". The order granting guardianship to the court was made for seven years as anything else was "at odds with that clinical reality".
The father said the judgment was "hard to accept". "The fact I know what they are giving him is not something that is doing him good."
He said he had not held out great hope of success but felt his strong beliefs needed to be put in court.
"I'm just a mere person. The applicants, these are doctors. The judge would go with the professionals."
He said he would abide by the court decision and a contract he had signed with the health board allowing treatment. "I have come to New Zealand. I've made New Zealand a home. [His son] was born here. This is his home. I am now a citizen of New Zealand. There are laws here which I need to abide to."
The father said he was considering the judgment and was concerned his son's views hadn't been considered at this stage. While he didn't know - and wouldn't know for another 18 months - he was HIV-positive, he should have been asked how he felt about receiving medication.
He was also concerned at anxiety on his son's part over the treatment he was receiving.
"My wife died when he was still young and since then there have been clinical appointments. Every three months they are taking the bloods.
"He thinks there is something terrible about him and that is why they are taking the bloods."
The recent hospital visit and subsequent medication had prompted the boy recently to ask: "Dad, when are they going to stop giving me these medicines. Is something wrong with me?"
He said the health board had sought, through the court, more than it had agreed when he signed a pre-Christmas contract allowing temporary treatment ahead of the court case. The agreement, he said, allowed reviews of treatment after 18 months or when his son's immunity levels rose to a specified level.
The man's lawyer said she was concerned there were not safeguards built in to recognise the child's rights.
