The 64-year-old researcher gained international fame in 2011 when he performed the world's first transplant of an artificial plastic trachea to be colonized by the patient's stem cells.
This experimental procedure was initially hailed as a great advance in the field of regenerative medicine before being disavowed because it was not based on sufficient foundations.
On Wednesday, the Stockholm Court of Appeal ruled that two of the three patients were not in a sufficiently serious condition at the time of the procedure, and "could have remained alive for a significant period without" it.
The third patient was in an emergency situation "but the procedure was still unjustifiable," the court continued, saying the surgeon acted intentionally.
"The intention to harm is the allegation, the most terrible accusation that can be made against a doctor," the fallen surgeon said at a press conference.
Contacted by AFP, Björn Hurtig, his lawyer, said he would appeal the judgment. "My client is very tormented," he said.
Paolo Macchiarini was a visiting researcher at the Karolinska Institute in Stockholm, from which the Nobel Prize in Medicine assembly emerged. Between 2011 and 2014, he operated eight people, three in Sweden and five in Russia.
Only one of his patients survived, after having the artificial trachea designed and implanted removed by the doctor during an operation in Russia in 2014.
All three patients treated in Sweden died, although the direct link between their deaths and the surgeries has not been established.
At first instance, the surgeon had been found guilty of "bodily harm" to a patient, the court considering that his interventions were contrary to generally accepted and scientifically approved practices.
The charges were dropped for the other two patients.
Convicted of scientific fraud by an external committee, he was dismissed from the Karolinska Institute in 2016.
The scientific publication The Lancet had withdrawn in 2018 two articles of the surgeon, published in 2011 and 2012.
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