Mounir al-Motassadeq is the only man to be convicted over the September 11, 2001 attacks against the United States.
However the court in Hamburg, northern Germany, ruled there was no proof of the 31-year-old’s direct involvement in the attacks that killed nearly 3,000 people in 2001.
Motassadeq has admitted to being friends with three suicide hijackers who took part in the September 11 attacks.
Presiding judge Ernst-Rainer Schudt gave no explanation for the court’s decision after the year-long retrial.
The Moroccan national was jailed for the maximum 15 years in February 2003 on more than 3,000 counts of accessory to murder and membership of a terrorist organisation.
However the conviction was quashed on appeal on the grounds that US authorities had refused to allow the court to question top Al-Qaeda suspects in custody.
Motassadeq was arrested in Hamburg two months after the September 11 attacks.
Prosecutors said he helped three Hamburg-based hijackers, including alleged ringleader Mohammed Atta, handled money transfers and covered up their whereabouts with full knowledge of their plot.
“The image of the naive, helpful student has been shattered,” chief prosecutor Walter Hemberger told the court in closing arguments last week.
He said the prosecution had successfully portrayed Motassadeq as a “radical Muslim engaged in holy war”.
But the defence claimed their client is innocent and was being tried for guilt by association.
While Motassadeq admitted attending mosque with the group and that he signed one of their wills, as well as visiting an al-Qaeda training camp in Afghanistan in 2000, he repeatedly denied any prior knowledge of the attacks.