Mr Malinauskas says he feels well, with just minor cold-like symptoms but has not indicated how he may have contracted the virus.
His wife and three children have all tested negative.
"This is an experience I share right now with thousands of other South Australians," he said in a statement on Monday.
"My thoughts are with every South Australian affected by this pandemic, whether it be those who have tested positive, those in isolation, families with holidays ruined, through to those businesses and workers who are grappling with the full impact of restrictions."
The Labor leader's case was among a record 2552 reported in SA on Monday with 94 people in hospital.
He was previously involved in a COVID-19 scare for a number of SA MPs in early December which prompted a brief shutdown of state parliament.
At that time, he was deemed a close contact of former premier Jay Weatherill who had contracted the virus at a school reunion in Adelaide.
The pair had dined together while Mr Weatherill was infectious but Mr Malinauskas subsequently tested negative.
SA then had just nine active virus cases after opening its borders to all interstate travellers late in November.
The state currently has more than 12,000 active infections.
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