Mother of two Mary Jane Veloso, 39, was arrested and sentenced to death in 2010 after the suitcase she was carrying was found to be lined with 2.6 kilograms (5.7 pounds) of heroin, in a case that sparked uproar in the Philippines.
She was due to take off on a Cebu Pacific flight to Manila shortly after midnight (1700 GMT) from Soekarno-Hatta international airport in the Indonesian capital Jakarta following an official handover signing.
"I have to go home because I have a family there, I have my children waiting for me," she told a press conference, adding that she wanted to spend Christmas with her family.
"This is a new life for me and I will have a new beginning in the Philippines."
The agreement between Jakarta and Manila states that she will be transferred as a prisoner but her sentence will fall under Philippine law upon her return, meaning President Ferdinand Marcos could decide to grant her a reprieve.
"I am very happy today, but to be honest I am a little sad, because Indonesia has been my second family," she said before singing the Indonesian national anthem.
"I hope you will all pray for me. I have to be strong."
The handover was attended by Indonesian immigration and corrections staff and representatives from the Philippine embassy in Jakarta and corrections officials from Manila.
Before addressing the media, she broke down in tears as she called her children and parents.
Veloso's travel document was stamped with a deportation mark and she will be banned from re-entering the country, according to Indonesian officials.
Her mother Celia Veloso, 65, has called for Philippine President Marcos to grant her clemency so she can spend Christmas with her family.
'Miracle'
Veloso told AFP on Friday in her first interview since the repatriation agreement that her release was a "miracle".
She was due to face the firing squad in 2015 but the Philippine government won a last-minute reprieve for her after a woman suspected of recruiting her was arrested and put on trial for human trafficking and Veloso was named a prosecution witness.
Showing off her traditional Indonesian batik creations, she said she had also learned guitar and how to play volleyball.
"I bring a lot of things, such as guitar, books, knittings... even this t-shirt I'm wearing was given by my friends," she said on Tuesday when leaving a Jakarta prison for the airport.
Muslim-majority Indonesia has some of the world's toughest drug laws and has executed foreigners in the past.
At least 530 people were on death row in the Southeast Asian nation, mostly for drug-related crimes, according to data from rights group KontraS, citing official figures.
According to Indonesia's Ministry of Immigration and Corrections, 96 foreigners were on death row, all on drug charges, as of early November.
Indonesia last week transferred home the five remaining members of Australia's "Bali Nine" and is in talks with France over the release of Serge Atlaoui, who has been jailed in the Southeast Asian archipelago since his 2005 arrest.
President Prabowo Subianto had agreed to fulfil their requests to hand back some prisoners who were sentenced on drug charges.
