In issuing its ruling on Monday, the Gothenburg District Court also convicted the woman of weapons crimes, sentencing her to probation and ordering that she undergo treatment for addiction and psychiatric problems.
The woman has continually denied committing any crimes, telling the local Göteborgs-Posten (GP) newspaper that she is an "odd bird" but that she is "not sexually interested in necrophilia".
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She had argued that she acquired the skeletons legally and that she handled the bones in a respectful manner and that her actions weren't covered by Sweden's laws against disturbing the peace of the dead.
But the woman was found to have kept some bones scattered on the floor in her home, stored skulls in plastic bags, and to have sold some bones to others.
"Criminal protection starts when a person dies, and the protection remains as long as there are remains of the deceased," the court wrote in a statement.
"The fact that the woman had moved bones constitutes a crime because she was unauthorized to do so, just as it's a crime to put together a skeleton and have it lying on the floor, to have bones in plastic bags, and to sell them."
According to the court, the 37-year-old handled the human bones "ignominiously", something which is prohibited by Sweden's laws against disturbing the peace of the dead.
The court added that the woman didn't need to be aware that her actions were criminal in order to be convicted.
"It's enough that she knew that she was handling human bones," the court said, explaining there was no doubt she was acting with intent.
However, the court threw out a charge stemming from allegations that she had stored human skulls in her freezer and used human bones for sexual purposes.
While the 37-year-old was facing up to two years in prison, the court ruled that her lack of criminal record and the nature of her crimes meant she should not be jailed, but instead be sentenced to probation.
The woman, who has continually denied any wrongdoing, was arrested in September when police arrived at her flat and found human skeletons and knives after responding to a call about gunfire coming from the apartment.