Veloso, a 39-year-old former domestic helper and mother of two, told reporters in Jakarta she was ready to start a new life in the Philippines.
Veloso was arrested in Yogyakarta in 2010 after being found with 2.6kg of heroin concealed in a suitcase. She said she was an unwitting drug mule, but she was convicted and sentenced to death.
Her release came days after the five remaining members of the so called 'Bali Nine' drug ring were repatriated to Australia from Indonesia.
Mary Jane Veloso says she is ready to start a new life in the Philippines. (AP PHOTO)
Veloso was flanked by heavy security upon her arrival at Manila's airport early on Wednesday and was transported straight to a prison facility for women.
Her family and dozens of supporters who were waiting outside the terminal failed to greet Veloso on her arrival.
"They made my daughter a criminal even if she is innocent. They did not allow us to see her. We wanted to hug her," her father Cesar Veloso told reporters at the airport as he broke down in tears.
Her mother Celia Veloso was more upbeat, saying: "What's important is she's here already".
Five Australians convicted of drug smuggling in Indonesia arrived home on Sunday. (Mick Tsikas/AAP PHOTOS)
Edre Olalia, Veloso's lawyer in the Philippines, said authorities had given her family private time with her at the prison facility.
The two governments agreed this month to transfer Veloso back to Manila in a deal that includes the Philippines respecting the court's sentencing of Veloso and her status as prisoner.
Any decision on her clemency will depend on Philippine President Ferdinand Marcos Jr.
Philippine executive secretary Lucas Bersamin said on Tuesday it's "premature to speculate" what Marcos will do.
Indonesia said it would respect any decision made by the Philippines, including if Veloso was given clemency.
Philippine Foreign Minister Enrique Manalo thanked the Indonesian government for its "sincere and decisive action" to allow Veloso to return home in time for the Christmas holidays.
"Their generosity has made possible this momentous day of Ms Veloso's return to the Philippines," Manalo said in a statement.
