The boy needed corrective surgery to repair the damage from the botched procedure.
In a 7-0 ruling from the bench, the justices left intact a Court of Appeal ruling convicting the man of aggravated assault and assault with a weapon.
The man, identified only as DJW, was convicted at trial in October 2009 of criminal negligence causing bodily harm and acquitted on the two assault charges.
The appeal court restored convictions on the assault counts and stayed the negligence charge, conditional on the conviction for aggravated assault.
The man's appeal to the Supreme Court sought to have the assault charges thrown out again, but the justices dismissed the case from the bench, saying their reasons would be available in 48 hours.
The original trial was told the man felt his religious beliefs required that his son be circumcised. Doctors advised him to wait until the child was older and stronger before performing the procedure.
In its factum on the case, the Crown dismissed the religious reasoning.
"This is a case about child abuse," the Crown argued. "This is not a case about the applicant's religious freedom or circumcision generally."
DJW's lawyer argued that the man took safety precautions, including extensive research on the topic of circumcision.
"The appellant's actions were performed with reasonable cause ... and without intent to assault or in any way harm his son," the factum said.
The trial judge found the kitchen was not a sanitary place for a surgical procedure, that the blade used wasn't as sharp as a surgical instrument and it was inappropriate to use a veterinary product to try and staunch the bleeding from the boy's partly severed foreskin.
DJW's religious background was as a Jehovah's Witness, although he was "disfellowshipped" by his family and the church. The Crown said his religious education and associations later led him to believe that male circumcision was a covenant with God.
He attempted to circumcise himself in 2005 and could not stop the bleeding. He had to go to an emergency room where a doctor sutured the wound.
His name is under a publication ban to protect the child's identity.