The Moroccan has admitted training at an al-Qaeda camp in Afghanistan and acknowledges he was close to the hijackers, but insisted he knew nothing of their plans.
Klaus Tolksdorf, the presiding judge, said evidence showed el Motassadeq knew they planned to hijack and crash planes.
He said his actions facilitated the attacks, and it was irrelevant to his guilt whether he knew of their timing, dimension or targets.
Tolksdorf said the evidence showed el Motassadeq helped "watch the attackers' backs and conceal them" by helping them to keep up the appearance of being regular university students.
"This is the day I've been waiting for for five years," said Dominic Puopolo Jr., an American co-plaintiff whose mother died in one of the planes that struck the World Trade Center in New York.
"This man's actions … caused thousands upon thousands of families untold grief, and to know that the German justice system has worked, it's a tremendously special day," Puopolo said.
There have been several setbacks in the pursuit of associates of the September 11 hijackers.
"Beyond this case, I can see now that the state of law has sufficient ability to deal with such extraordinary crimes," said Gerhard Altvater, a federal prosecutor, after the verdict.
El Motassadeq, who has already spent a total of about three years in prison, has been free since February pending the appeals process.
Altvater has considered bringing the Moroccan back into custody ahead of the sentencing hearing, which is expected to last only a few days. No date has been set for that hearing.
The Moroccan is one of only a few 9/11 suspects to have been tried worldwide. In the US, Zacarias Moussaoui, a French citizen of Moroccan descent, is serving a life sentence as a conspirator in the plot.
El Motassadeq was convicted of membership of a terrorist organisation and thousands of counts of accessory to murder in 2003.
He became the first person convicted anywhere on 9/11-related charges, and received a maximum 15-year sentence.
Ladislav Anisic, a lawyer for el Motassadeq pledged that "the defence will continue to pursue its efforts to secure an acquittal".
Hamburg authorities have said that, once legal proceedings against el Motassadeq are over and his sentence served, they will deport him to his native Morocco.