Although Mount Barker Road was reopened to traffic, speed restrictions remained in place, and a cordon surrounded the shopping complex.
CFS spokesperson Cameron Devey said that aerosol canisters were reportedly exploding before emergency services arrived on the scene.
Fire Cause Investigators conducted an initial assessment, but a more detailed investigation will be carried out to determine the exact cause of the fire.
South Australian police have confirmed that the two 14-year-old boys, from Heathfield and Bridgewater, will be charged with arson relating to the supermarket fire.
They will be granted bail and are expected to appear at the Mount Barker Youth Court in December.
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