The teenager, again donning the mask he has worn during the past two months to shield himself from cameras, was accompanied by his father to the prison where the pair had to run the gauntlet of a large media presence.
He was then removed by immigration officials to an office near the airport ahead of his deportation to Australia.
His lawyer, Mohammad Rifan, who met the boy at the prison and followed him to the immigration facility, said an airline ticket had already been purchased so the boy could return home later on Sunday.
"He is very happy ... he will go home today," Mr Rifan told reporters.
"He's very happy to be going to meet his family and friends, even though he is still in a little shock after his time in Bali."
The teenager has been in custody since his arrest on October 4, when he was caught with 3.6 grams of marijuana, which he later confessed to buying from a dealer on Kuta Beach.
He was sentenced last week to two months in prison after being convicted on one count of drug use, but was eligible for release on Sunday owing to time already served.
The drug-use charge carried a maximum penalty of two years for juveniles but no minimum term. He had also been facing a possession charge which could have seen him jailed for up to six years.
While he was sentenced to a prison term, the boy was allowed to remain at the immigration facility in Jimbaran after Indonesia's Justice and Human Rights Minister Amir Syamsuddin intervened and ruled that Kerobokan was not suitable.
His parents were also allowed to stay with him at Jimbaran.
The lenient treatment afforded to the boy and his family was met with criticism in Indonesia after it was revealed nine Indonesian children were being held in Kerobokan, which houses drug traffickers, sex offenders and murderers.
The governor of the prison, Siswanto, said he believed the schoolboy, who admitted during his trial to being a long-term drug user, had learnt from his horror experience in Bali.
"Today he is free," Siswanto said.
"I gave him advice not to be involved in drugs again."
- AAP