The brothers, aged 16 and 17, raised suspicion when they attempted to pass through customs, Immigration Minister Peter Dutton said on Sunday.
"What we have here are two teenagers who have been intercepted on their way to a potentially very dangerous situation," Dutton said.
The teenagers had return tickets to unnamed "conflict zones" in the Middle East, and a luggage search heightened suspicions that they were headed abroad to fight.
The boys were later released into the custody of their parents, who were said to have no idea of their intentions.
"These two young men...are kids, not killers," Dutton said, who added the matter had been referred to the Australian Federal Police.
Prime Minister Tony Abbott said the brothers were Australian citizens who had been lured by a "death cult."
"These were two misguided young Australians, Australian born and bred, who went to school here, grew up here, imbibed our values, and yet it seems they had succumbed to the lure of the death cult and they were on the verge of doing something terrible and dangerous."
The prime minister spoke directly to other susceptible Australians who were considering leaving to fight abroad.
"My message to anyone who is listening to the death cult is block your ears. Don't even begin to think you can leave Australia," he added.
Australia estimates there are at least 90 citizens fighting and supporting terrorist groups in Iraq and Syria.
Last month, the government announced plans
to suspend or revoke citizenship for dual nationals involved in terrorism, and also strip certain privileges from Australian citizens who break anti-terror laws.