Pfäffikon district court convicted the woman of murder and grievous bodily harm in the verdict on Tuesday, newspaper Zürcher Oberlander reports.
At the time of the incident in 2006, the woman lived in a religious sect in the Zurich Oberland as the girlfriend of the victim's father, a man referred to in the Swiss media as Hash-Jesus.
The 44-year old disciplinarian, who thought he was the son of God, was sentenced to nine years and six months imprisonment in 2010 for repeatedly beating his deceased daughter and her older half-sister, who survived the ordeal.
The court found that he had given the girls a sadistic upbringing through the use of a punishment system based on the Old Testament and designed to break the will of the children, who lived in “permanent fear“.
A 62-year old female social worker who lived with couple was also jailed for seven years for her part in the abuse.
The sect leader’s girlfriend admitted to the court that she used all her strength to shake the child in May 2006 in what she described as “an unintentional emotional reaction“ after the girl wet her pants.
The judge said the woman must have known that the brutal treatment of the children was wrong and ought to have “recognised the hunger and bruises“ of the children to whom she was a “virtual mother“.
The court found that she actively supported her boyfriend's cruel regime as she did not want to lose him. The accused, whose gender was uncertain at birth, was baptized as a boy. She became acquainted with the girls' father shortly after travelling abroad to undergo a sex change operation.
The state prosecutor had called for a 16-year sentence, but the judge took the woman’s remorse over the death of the almost 5-year-old girl into account.
Her lawyers had called for two years, arguing she was not as guilty as her accomplices as she was only “part of the system.“
The ex-girlfriend said she has now distanced herself from the teachings of the sect leader.
The court set compensation for personal suffering for the surviving child at 30,000 francs ($33,600) to be paid by the woman and 75,000 ($83,950) to be paid jointly with the girl's father and the ex-social worker.