The man in his 80s is recovering at home after being discharged from hospital.
There have now been 10 confirmed cases of the virus in the state this year, including two deaths.
The latest infection follows warnings that flooding down the Murray River will increase the risk of outbreaks.
A large-scale vaccination program has been put in place for river communities and for emergency service workers responding to the flood emergency.
Chief Public Health Officer Nicola Spurrier urged people to take extra precautions against mosquitoes this summer, with flooding and warm weather widespread across many parts of the state.
"People planning activities around the Murray and Lower Lakes are warned to be especially vigilant, particularly between dusk and dawn when mosquitoes are most active," Professor Spurrier said.
"If you are outside, apply an insect repellent containing DEET, picaridin or oil of lemon eucalyptus.
"Simple changes around the home can help to reduce and eliminate mosquitoes such as cleaning up water around the house to prevent mosquito breeding, and installing mosquito-proof mesh on doors and windows."
SA Health said mosquitoes could also carry other viruses including the Ross River virus, Murray Valley encephalitis virus, West Nile virus and Barmah Forest virus.
It said taking steps to avoid bites was extremely important, advising people to cover up with light-coloured, long-sleeved, loose-fitting clothing and to regularly apply insect repellent.
Symptoms of Japanese encephalitis include confusion, headaches, tremors, drowsiness, neck stiffness and seizures.
While most people infected will not experience any or only mild symptoms, a small number will develop an inflammation of the brain, which can be fatal or cause long-term neurological damage.
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