The motion called for the Scottish Government to look at how the justice system could better understand and respond to individuals with autism as they interact as witnesses, victims, suspects or offenders.
The motion was the first time that a stand-alone motion on autism had been tabled at any party conference, according to the National Autistic Society.
Commenting afterwards Mr McDonald said:
"This was a historic moment for the campaign to raise awareness and understanding of autism across Scotland. I am delighted that SNP conference backed this motion unanimously.
"There is tremendous work going on throughout Scotland to raise awareness of autism and to ensure that services are tailored to meet the needs of individuals on the spectrum.
"I felt that criminal justice was an important element of the equation that needed more consideration. Many on the autistic spectrum can make credible witnesses, but how they are questioned is very important. It is also important that behaviours borne of an autistic spectrum disorder, that could be interpreted as suspicious or indicative of guilt, are better understood.
"I hope that now we will be able to develop appropriate understanding of how our justice system approaches individuals with autism at all levels."
Gillian Martin added:
"Interaction with the justice system can be stressful enough, when you have a condition that can make your behaviour unpredictable in the face of such stress it can complicate matters.
"What we need is an understanding of how to appropriately approach, question and, where necessary, rehabilitate individuals with autism who come into contact with the justice system.
"I was delighted to back this important motion and I look forward to supporting progress on these issues over the months and years ahead."