"After 20 years, I can finally return to the life that I deserve," Aoki told reporters.
"I can hear my daughter saying to me `Mom, I`m happy for you`. I want to tell her `thank you` for watching over me all this time."
The couple had been found guilty of setting their house on fire by spraying gasoline in the garage a blaze that killed Aoki`s daughter Megumi in an attempt to claim insurance money.
But a court in Osaka on Friday upheld a lower court`s decision to order new trials in the case amid serious doubts about the couple`s guilt.
It was not clear why there was a delay between Friday`s decision and their release.
Defence lawyers had argued that subsequent tests suggested the fire was likely not arson, and there were questions about whether the boyfriend was forced into a false confession during his interrogation.
Prosecutors had also failed in their attempts to re-create the fire with key details from his original confession, reports said.
Their release comes after Iwao Hakamada believed to be the world`s longest-serving death row inmate walked free from jail last year after decades in solitary confinement, in a rare about-face for Japan`s rigid justice system.
He had been accused of being responsible for the grisly 1966 murder of his boss and the man`s family, but doubts arose about the reliability of his confession.
Confessions are common in Japanese criminal cases and typically seal the fate of almost all those charged with crimes.
Masaru Okunishi, who had spent decades seeking a retrial while sitting on death row, passed away this month at the age of 89.
He had been convicted of multiple counts of murder for slipping pesticides into wine at a community party in a remote mountain village in the early sixties.
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