Abd al-Ghani Mazwadi was also found not guilty on a lesser charge of terrorist organisation membership by the Hamburg court this Thursday.
Mazwadi showed no immediate reaction when the verdict was finally handed down, despite being cleared of more than 3000 counts of accessory to murder - a number based on the 9/11 death toll.
He could have faced up to 15 years in jail if convicted when prosecutors charged Mazwadi provided logistical support for a Hamburg al-Qaida cell.
The presiding judge said Mazwadi was no longer a prime suspect as there was a "serious possibility" he had been "deliberately excluded" from planning for the attacks.
But the case has shown significant weaknesses, dogged notably by a lack of direct evidence and the refusal of US authorities to release evidence.
Court room drama
The court's decision had been delayed by a last-minute challenge from a lawyer representing some of the victims - but not from the chief prosecutor.
Families of 9/11 victims claimed new evidence linked the 31-year-old Moroccan to another alleged conspirator Zakariya Musawi.
But judges rejected that challenge made by lawyer Andreas Schulz.
Only two people have ever gone
to court for 9/11
His last minute submission centred on evidence reportedly given by alleged al-Qaida operative Ramzi al-Shibh to his US captors.
Al-Shibh claims he was part of the tight-knit Hamburg group that included Mazwadi and three 9/11 hijackers, including suspected ringleader Muhammad Atta.
However US authorities have repeatedly rejected court requests to allow al-Shibh to testify in Germany, or at least to use his evidence, despite Schulz saying there was now "an apparent change in the US position."
He claimed that US prosecutors had indicated they would use testimony from al-Shibh in the upcoming trial of Musawi, who is alleged to have been a would-be 20th hijacker.
But presiding judge Klaus Ruehle made clear his scepticism over a late appeal by victims' families after Schulz said he was "not authorised" to divulge where his information had come from - to the judge's clear frustration.
The court then refused any new attempt to approach US authorities after chief prosecutor Walter Hemberger also said he was unaware of any shift in attitude by US authorities.
But prosecutors say they are confident of a successful appeal, with Hemberger adding that there were "numerous grounds" to believe that he was involved in plotting the suicide plane strikes in New York and Washington.
"We are convinced that the accused was guilty," he told a press conference after the verdict. "We will therefore lodge an appeal."
He said he would await the court's written judgment before establishing the exact grounds for an appeal. Prosecutors have a week to make a decision.
In possible support, judge Ruehle said the court had decided on its verdict not "because it was convinced of the innocence of the accused, but because there was not enough evidence for a conviction."