In finding the 13-year-old accused not guilty, Justice Mary Teresa Devlin said she had doubts about the identity of Mitchell Wilson's attacker.
"I believe they followed the law right to the letter (and) I don't think Mitchell would've liked to have seen the law bent for his own benefit," his father Craig Wilson said outside court.
"For that reason, I think we walked out respectfully with our heads held high."
Mitchell, who suffered from muscular dystrophy, killed himself last September, after being subpoenaed to testify in the case.
His family said he was terrified at the prospect of facing the youth accused of slamming his face into the sidewalk, chipping his teeth, and stealing his iPhone in Pickering, Ont., in November 2010.
Mitchell faced constant bullying, and the assault on top of his progressive muscle-wasting disease had plunged him into a downward spiral of despair, his family said.
He died last Labour Day after wrapping a plastic bag over his head.
The case drew the attention of Premier Dalton McGuinty, who cited it along with other similar high-profile cases, as reasons to implement tough anti-bullying legislation.
Last month, Devlin admitted oral and written statements as to the identity of his attacker that Mitchell had given his stepmother and police before his suicide.
Craig Wilson said his son was certain he had accurately named his assailant, who cannot be publicly identified because of his age.
However, in court Monday, Devlin said Mitchell's identification of the accused could have been faulty, and therefore she had no choice but to issue the acquittal on charges of assault causing bodily harm and robbery.
She also said she hoped those responsible would have the courage to come forward and take responsibility for their wrongdoing.
Afterward, his aunt Cheryl Wilson said the family had wanted Mitchell's voice heard.
"I don't think we were looking for any sort of retribution or anything," she said.
"Since he wasn’t here, we were here as a family to follow it through court right from the beginning until the end."
She also said the family was leaving court with "the same great memories we had coming in of a wonderful little boy."