The jury took two hours to reach the verdict on which another jury was hung at the end of the first trial in November, 2011.
It related to Sahara's death on the night of December 20, 2010, while Ms Baker was at work at The Warehouse.
Ratana was looking after Sahara, her 7-year-old sister, and the couple's 2-year-old son in their Onekawa flat.
When Ms Baker returned home after 10pm, Sahara was dead, with her sister asleep in the same room.
The mother, who presumed the children were asleep, knew nothing of the horror on the other side of the wall until she heard Ratana in a distressed phone discussion with his father.
Unable to get an explanation and suddenly fearful about what might have happened, she went to the bedroom, and found the cold body of Sahara.
Ratana admitted causing the girl's death by pressure to her chest, but denied any sexual violation.
In his closing address, Crown prosecutor Clayton Walker focused on evidence of the girl's internal genital injuries, saying experts established they were highly unlikely to have been present before Ms Baker went to work, nor caused by accident, and, therefore, must have been caused by Ratana.
Defence counsel John Rowan QC focused on Ratana's three co-operative interviews with police, denying any sexual violation and saying Ms Baker must have been mistaken in her assertion that Ratana told her when she discovered Sahara dead in the girl's bed that he had raped her and was sorry.
Mr Rowan also highlighted a Crown decision to amend the charge from rape (meaning forced sexual intercourse) to one of sexual violation by unlawful sexual connection, alleging penetration with a penis, finger or similar shaped object.
He claimed the change, before the first trial, lessened the strength of the claims against Ratana.
Experts were unable to time when the injuries might have been caused, but Mr Rowan said it had been established other children had been playing with Sahara in the hours before her mother went to work, and the bruising could have been caused at that time.
Ratana would be sentenced on both charges on April 27.