His family picked him up from a jail on the outskirts of Jakarta, the capital of Indonesia, at 05:24 local time, a spokesperson told BBC Indonesia.
The 82-year-old was formerly the commander of Jemaah Islamiah, an al-Qaeda-inspired group that was blamed for the attack that killed 202 people.
He has been released after his sentence was cut short.
People from 21 nations died in the blasts on 12 October 2002 in the popular holiday island of Bali. The two bombs ripped through Paddy's Irish Bar and the nearby Sari Club in the Kuta tourist district.
It was Indonesia's worst terrorist attack.
The decision to release Ba'asyir has drawn mixed reactions in Indonesia as well as Australia, where most of the victims were from.
Ahead of his expected released Garil Arnandha, whose father was among the victims of Bali bombings told the BBC: "I don't agree with Abu Bakar Ba'asyir being released because in my opinion he is still very dangerous and has the potential to revive terrorism in Indonesia."
Endang, his mother, had a different view.
"As a bomb victim I have forgiven him," she told the BBC.
"He has served time in jail for his crimes and I really hope he will return to the right path. I am worried but I am trying to have positive thinking because the trauma of losing my husband in the bombing has been horrific."