The appeals court on Thursday rejected an appeal from federal prosecutors for a new trial, citing a lack of evidence.
The court therefore confirmed the judgment of the Hamburg appeals court which acquitted Mzoudi in February 2004.
Mzoudi, 32, had been tried in Hamburg in 2003 but his trial collapsed.
Mzoudi lives in Hamburg, the northern German port city which was one of the planning nerve centres of the aeroplane attacks on the World Trade Centre and the Pentagon which killed around 3000 people.
Prosecutors had said Mzoudi was part of a Hamburg cell.
Another Moroccan, Mounir El Motassadeq, is currently in the
middle of a retrial on similar charges. He is being held in
Motassadeq denies having any knowledge of the planning for the attacks.