Police will allege the duo intended to cause harm to 'a large number of people' at the high school in the state's Riverland region.
Searches allegedly discovered knives, and homemade body-armour and bombs.
It is believed the teenagers were planning an attack involving explosives and knives at the school between June 1 and November 7 this year.
One boy, 16, has been charged with solicit to murder while the other, 18, has been charged with four counts of aggravated threats.
Detective Superintendent Des Bray, head of South Australia's major crime branch, said the planned massacre would have been 'catastrophic' and added it was likely it would have been carried out had it not been stopped by police.
'We believe there was a real threat, actively planned and likely to be carried out without the actions of police,' Superintendent Bray told reporters.
'It is unbelievable to think this kind of thing could have happened in South Australia.
'I'm extremely grateful of the response of the local police and there is no doubt we prevented a catastrophe.'
He said police became aware of the planned massacre after the teenagers began to tell others what they intended to do.
Superintendent Bray explained, 'They told some other people about what they were intended to do, and then they told other people.
'Soon it became known to quite a number of people. It is believed there were no specific individuals targeted but the faculty and students.'
He urged anyone who had further information on the alleged attack to contact police.
Anyone with information is urged to call Crime Stoppers on 1800 333 000.