Mounir el Motassadeq was sentenced in January 2007 by a German court to 15 years in jail for his role in the death of 246 passengers and crew aboard hijacked aircraft used in the September 11th attacks.
He was the first person ever convicted for complicity in the attacks on the Twin Towers of the World Trade Center and the Pentagon.
The Moroccan was put on a plane at Frankfurt's airport on Monday and sent back to his country of origin, according to an airport police spokesman, speaking to the German national news agency DPA.
Several police officers accompanied him. Earlier he had been taken by helicopter from the Hamburg jail where he has been serving his prison term to Frankfurt, according to Spiegel Online and Bild daily.
Photographs carried by DPA showed him dressed in a checked shirt and beige trousers, being led blindfolded and handcuffed by two police officers to a waiting chopper.
Frank Reschreiter, Hamburg Interior Ministry spokesman, confirmed that el Motassadeq would be leaving Germany on Monday.
He said: "All the necessary procedural steps for this have been ticked off according to plan."
Motassadeq, who was held in prison just after his arrest in Hamburg in late 2001, had served nearly all of his sentence.
SEE ALSO: Germany to expel 9/11 accomplice to Morocco
El Motassadeq had come to Germany in 1993 to study engineering. The Moroccan was friends with members of a Hamburg-based cell, including their leader, Egyptian Mohammed Atta.
Atta was ringleader of the 9/11 hijackers - and he himself had hijacked the American Airlines Flight 11 and crashed the plane into the North Tower of the World Trade Centre as part of the coordinated attacks.
El Motassadeq has admitted to having links to the hijackers, but he maintained his innocence in a five-year court battle.
He became a suspect after German police realized he held power of attorney over a bank account belonging to Marwan al-Shehhi, the terrorist who flew United Airlines Flight 175, into the south tower of the World Trade Center.
He helped to cover up the hijackers' whereabouts by paying their tuition fees and rent to keep the pretence that they were students while they were taking flying lessons in the U.S. and handled a bank transfer for them.