Imad Yarkas, the accused cell leader, was sentenced to 27 years in prison.
The verdicts were read out at the National Court in the conclusion of Europe's biggest trial of al Qaeda suspects.
Prosecutors had accused Yarkas, a 42-year-old Spaniard of Syrian origin, of being an accomplice to murder and requested a jail term of nearly 75,000 years — 25 years for each of the nearly 3,000 people killed in the suicide airliner attacks in 2001.
But in the end, he was convicted of the lesser charge of conspiracy.
Yarkas, a father of six, had been charged with arranging a meeting in the Tarragona region of Spain in July 2001 at which key Sept. 11 plotters — alleged suicide pilot Mohamed Atta and plot coordinator Ramzi Binsalshibh — met to decide last-minute details, including the date of the massacre.
Another suspect, Moroccan Driss Chebli, was also alleged to have helped set up the meeting. He was acquitted on Monday of murder charges but convicted of collaborating with a terrorist group and sentenced to six years.
The third suspect facing specific Sept. 11 charges, Ghasoub al-Abrash Ghalyoun, was acquitted Monday. The Syrian-born Spaniard was indicted over detailed video he shot of the World Trade Center and other landmarks during a trip to several U.S. cities in 1997.
Judge Baltasar Garzon had said the tapes were passed on to al Qaeda and amounted to the genesis of planning for the attacks on the U.S. Ghalyoun said during the trial he shot the tapes as an innocent tourist.
Ghalyoun was also acquitted of charges of being a member of a terrorist organization.
Spain is the second country, after Germany, to try suspects in the suicide airliner attacks against the World Trade Center and the Pentagon in 2001.