The B.C. Court of Appeal has stayed the man's conviction for criminal negligence causing bodily harm and convicted him of aggravated assault.
Court heard the boy was born premature at only 2.5 pounds and could not be circumcised at the time, nor did his parents request it.
But the court found the boy's father "changed his world view" over the ensuing years.
"He came to understand that there was great utility in keeping the laws of Moses including that of circumcision," the appeal ruling said.
The trial judge found "that the accused decided that because so many disasters had befallen his family, he had to 'make things right with God.'"
The man, who had no medical training, tried to do the circumcision in 2007 after doctors refused to do it on the grounds the operation would require a general anesthesic, which couldn't be justified on a boy that age.
Court documents say the man gave alcohol to the boy, referred to only by the initials D.J., and used a blade that was not as sharp as a surgical instrument. To staunch the bleeding, the man used a veterinary powder suitable only for livestock.
The boy was taken to hospital four days later and required corrective surgery, including a proper circumcision. The surgeon testified his penis would have healed to be badly deformed.
Among her reasons for convicting the man, the trial judge, who is not named, noted that the man had tried to circumcise himself a few years before he undertook the procedure on his son.
His actions caused "his foreskin to bleed in nine places, requiring the assistance of 911 and sutures in hospital," resulting in an infected penis.
"The accused was aware of the dangers of performing a circumcision on his son," the trial judge wrote.
The man, who was not named, was charged with criminal negligence causing bodily harm, aggravated assault and assault with a weapon for the incident with his son..
At the man's original trial, the judge in the case convicted him on the negligence charge but acquitted him on the assault charges.
He appealed his conviction, arguing his religious beliefs should have allowed him to do the procedure, but the Appeal Court rejected the appeal.
"The accused’s religion did not demand that the circumcision be performed by the accused himself, nor did the trial judge find that religious necessity dictated that the circumcision be performed immediately so that the accused was left with no alternative but to perform the operation himself," the appeal court ruling said.
"Thus, it is not the accused’s religious beliefs that are at issue, but the rights and best interests of D.J. with respect to whether he should have been subjected to an attempted circumcision by his father in the circumstances and conditions under which it was attempted."
The Crown appealed the acquittals on the assault charges and while the appeal court rejected the charge of assault with a weapon, it imposed a conviction on the charge of aggravated assault.
The court has ordered new sentencing for the man, who was originally given two years in prison under the criminal negligence charge.