Mussie Debresay was jailed for 11 years for killing the toddler in his Footscray unit in May 2005.

A Supreme Court jury had accepted that Mr Debresay, acting in anger and frustration, had stomped on the girl's abdomen after she urinated on his couch. She died of serious internal injuries.

In a dramatic decision on Thursday, three Court of Appeal judges overturned Mr Debresay's manslaughter conviction.

The little girl, who cannot be named for legal reasons, was the daughter of Mr Debresay's partner.

Evidence from the girl's brother, who was four years old when he witnessed the attack, was crucial in Mr Debresay's trial.

But Court of Appeal justices, Phillip Priest, David Beach and Stephen Kaye, AM, said the brother's evidence was unreliable and the jury could not have found Mr Debresay guilty beyond reasonable doubt.

"We have concluded that the jury, acting reasonably, must have had a reasonable doubt as to the applicant's guilt," they said.

"In our view, it simply was not open to the jury to convict the applicant.

"We have a reasonable doubt about the applicant's guilt."

They said the jury could not have concluded whether Mr Debresay or the toddler's mother killed her, based on her son's evidence.

"On all of the evidence, however, we think it impossible to exclude beyond reasonable doubt the reasonable hypothesis that [the toddler's mother] caused the injuries.

"But as we have concluded, the jury could not reasonably have been satisfied beyond reasonable doubt that she did not," they said.

"The verdict is unsafe and unsatisfactory. It must be set aside."

Mr Debresay faced court on Thursday morning via video link from prison. He was expected to walk free in the afternoon.

In September last year, a Supreme Court jury found Mr Debresay not guilty of the charge of murder, but guilty of the alternative, less serious crime of manslaughter.

Mr Debresay had maintained his innocence throughout his trial, telling police that the toddler had fallen in his living room that night.

He allegedly attacked the girl in the kitchen of his home.

The toddler's brother told police and family members in a number of recorded interviews since 2005 that Mr Debresay hurt his sister after she had been sick and urinated on his couch.

The boy maintained this a decade after the alleged attack but during the trial he conceded under questioning from Mr Debresay's lawyer, Dermot Dann, QC, that on the night his sister died he did not see the actual attack.

In 2013, the state coroner found him and the girl's mother jointly responsible for the toddler's death, either through their actions or inaction, in failing to get medical help sooner.

Both refused to give evidence at the inquest for fear of self-incrimination. The mother was never charged.

When he sentenced Mr Debresay in December last year, Justice Terry Forrest said it was not his job to sentence the woman "for her many failings as a mother".

She became infatuated with Mr Debresay after they met in early 2005, the judge said, and this had compromised "whatever parenting skills she had".

Mr Debresay, who came to Australia from Eritrea as a teenager, has a daughter with his victim's mother and a teenage son from another relationship.

The toddler's mother was still in a relationship with Mr Debresay when he was sentenced last year.