Phillip Seaton had argued his penis was removed without his consent during what was supposed to have been a circumcision to treat inflammation.
Dr John Patterson said he had found life-threatening cancer during the procedure and saved Mr Seaton's life.
The Seatons had asked for $16m (£9.8m) for "loss of service" and "love".
They had already sued Jewish Hospital, where the surgery took place; the facility settled out of court for an undisclosed amount.
After brief deliberations on Wednesday, the jury ruled unanimously against the Seatons' claim that Dr Patterson had not exercised proper care, but split 10-2 against a claim Mr Seaton had not consented to the amputation.Dr John Patterson (right, with his lawyer last week) says he found cancer during the surgery
In court filings, the Seatons argued Mr Seaton should have been awakened from anaesthesia and consulted before Dr Patterson did the surgery.
Clay Robinson, a lawyer for Dr Patterson, argued his client had only removed about an inch of the penis after finding it riddled with cancer, with the rest amputated by another doctor.
He also contended Mr Seaton had signed a document authorising necessary treatment in unforeseen circumstances.
Penile cancer is rare, with only 1,360 new cases and 320 deaths estimated in the US in 2011, according to the National Institutes of Health.