Mounir el Motassadeq was sentenced to seven years in prison last August by a court in Hamburg.
City judicial spokesman Carsten Grote on Tuesday said Germany's Federal Constitutional Court has now ordered him released. Grote did not give a reason for the higher court's decision.
It was not clear when el Motassadeq, 31, would be released.
In 2003, the Moroccan became the first person anywhere to be convicted with the 9/11 hijackings when he was found guilty of membership of a terrorist organisation.
Another federal court overturned his conviction the following year, and ordered his retrial. He was again found guilty. Appeals from both his defence lawyers and prosecutors are still pending.
El Motassadeq was accused of helping to pay tuition and other bills for cell members to allow them to live as students while they plotted the attacks. Prosecutors had demanded his conviction on all the charges and the maximum sentence of 15 years in prison.
The Moroccan acknowledges he was close to the hijackers but insists he knew nothing of their plans. He spent some two-and-a-half years in prison between his November 2001 arrest and his release in April 2004, and has been jailed again since his conviction last August.