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Instead a jury in the High Court at Auckland found her stepfather Michael Joseph Martin, 25, not guilty of murdering her.
It also found him not guilty of manslaughter, and not guilty of ill treatment or neglect of a child for failing to provide Leilani with medical assistance.
The Crown said Martin struck the then-toddler's stomach with a blow so severe it ruptured an internal organ and a resulting infection proved fatal.
The defence said Martin was innocent and Leilani's mother Amy Lorigan must have been responsible.
After hearing eight days of evidence, Justice Graham Lang summed up yesterday, telling jury members the Crown case was circumstantial and they must be sure Martin delivered the blow and knew he was causing harm that could kill if he was guilty of murder.
A finding of manslaughter was also available, he said.
Earlier defence lawyer Michele Wilkinson-Smith said the case against Martin lacked evidence and was just a theory.
Martin did not know who injured Leilani and when told of her injuries was "lost for words", she said.
Crown prosecutor Christine Gordon, QC, said in her closing that Martin struck Leilani when Ms Lorigan was out shopping between about 12 and 1pm on June 9, 2012.
Ms Gordon said Martin's conduct in an interview with police was contrived and lacking emotion.
He did not give evidence at his trial.
Leilani was pronounced dead just before 6am on June 10, 2012, when paramedics were unable to save her.
- By Jimmy Ellingham and Patrice Dougan of APNZ