"In this case, a woman of unknown ability used a sharp implement to excise the clitoral hood of each girl," Justice Clare said during sentencing on Thursday.
"The girls were not sedated, there was bleeding and a period of significant pain for perhaps a number of days, there was obvious risk of infection, even death."
She is the first person to be sentenced in Queensland for removing a child from the state for female genital mutilation.
Cutting or removing some of a girl or young woman's genitals is considered traditional in some cultures but illegal here.
"To treat the adherence to tradition as mitigation would dilute the protection of the law for those children in most need of it," Justice Clare said.
"No matter where a family may come from, whether it be Somalia, India or Ashgrove, it makes no difference, that children in this state have equal protection under the law."
The girls were playing outside their grandmother's home days after arriving in Somalia when they were separately called inside.
A woman they didn't recognise carried out the procedure on the older girl first, followed by her younger sister.
Their stepsister tipped off child safety services when they returned to their home south of Brisbane several months later.
Knew it was illegal
Crown prosecutor Dejana Kovac said the mother told a child safety officer in 2008 that she knew genital mutilation was illegal here, that sending children overseas to have it done was also against the law and she did not intend to subject her daughters to it.
Ms Kovac said the woman had her daughters subjected to genital mutilation despite undergoing the procedure herself and experiencing complications because of it.
The woman's children were in court for the sentencing, and her eldest son at one point got on his feet in the public gallery to ask if he could speak.
Judge Clare told him he could not.
Defence barrister Patrick Wilson said the children stood by their mother, who is undergoing chemotherapy for breast cancer that has spread to her spine.
He said his client was often in pain, that she found it difficult to walk and breathe, and suffered significant swelling in her arms.
The children will be cared for by their father, and the woman's sentence will be suspended after eight months.