The doctor was on trial in Geneva nearly three years after the incident in July 2014.
The young victim was taken by his parents to the doctor's Geneva surgery to be circumcised, an event considered by many faiths as a ritual to be celebrated.
During the operation the boy's father was taking photos. At the crucial moment he raised his hand to take a photo and his son turned towards him, moving his pelvis and causing the surgeon to severe the penis which fell to the floor.
The prosecutor in the case claimed the surgeon then tried to cover up his mistake by spending hours searching for the necessary equipment to reattach the boy's penis instead of sending him straight to hospital.
However defence lawyer Charles Joye said his client told the father to take his son to Geneva University Hospital (HUG) immediately, and that he could not be held responsible for the “unforeseeable act” – meaning the taking of photos – that caused the accident.
In its judgement on Tuesday the court said the factors involved had made the accident “unforeseeable”, reported Le Temps.
The 59-year-old surgeon had not violated medical rules by attempting to reattach the penis, even though that solution was not “ideal” said the court, particularly because he did not have the right equipment to hand.
Speaking after the court's decision on Tuesday Joye said: “The court recognizes that the surgeon is not responsible when an unforeseeable event, such as in this case, causes an imprecise action.”
He added: “The event that took place was an unfortunate accident, not caused by the doctor, and his behaviour testifies to his cool head as well as his skill”.
However the judgement was criticized by the lawyer of the boy's parents, who said the court ignored the fact the doctor created an unsafe situation by letting the victim's father take photos “certainly for commercial ends”.