Shizuoka District Court suspended the death sentence for 78-year-old Iwao Hakamada, a former professional boxer convicted of the 1966 murder of a family, and ordered a retrial.
More than 45 of the 48 years Hakamada has spent in jail have been on death row, making him the longest-serving such inmate, according to Guinness World Records.
Hakamada was sentenced to death in 1968 but was not executed because of a lengthy appeals process. It took 27 years for the supreme court to deny his first appeal for a retrial. He filed a second appeal in 2008, and the court finally ruled in his favour.
The court said DNA analysis obtained by Hakamada's lawyers suggested investigators had fabricated evidence. It ordered a retrial, making Hakamada only the sixth death row inmate to get a retrial in post-war Japan.