Osama Awadallah, 26, turned to look at his crying father as the verdict was read. Jurors began deliberating Thursday.
"I knew that justice would prevail," he said to reporters. "My goal will be to continue to be a very good citizen in this country."
A first trial last springafter the jury deadlocked 11-1 for conviction. In contrast, this jury decided to acquit on its first full day of deliberations, CBS News reports.
Awadallah was detained 10 days after the Sept. 11 terrorist attacks and held as a material witness for three weeks while investigators looked at his friendship with one of the hijackers.
Awadallah had lived in the same San Diego community as Nawaf al-Hazmi, who helped seize the plane that crashed into the Pentagon. They attended the same mosque and saw each other dozens of times in 2000 before al-Hazmi moved to Virginia. FBI agents became curious about Awadallah when they found his phone number in al-Hazmi's car.
Investigators ultimately decided the two men were merely acquaintances, but Awadallah was charged with perjury over two statements he made to a grand jury on Oct. 10, 2001.
During testimony, Awadallah said he could not remember the name of a man he frequently saw with al-Hazmi, who authorities believed to be fellow hijacker Khalid al-Mihdhar.
When confronted with a school examination booklet in which he appeared to have written about meeting men named Nawaf and Khalid, Awadallah initially claimed it was not his handwriting.
Later, he returned to the grand jury and said he had been mistaken on both accounts. He did recall meeting someone named Khalid, and he had written that name in his booklet.
Prosecutors said Awadallah had intentionally tried to minimize his relationship with the hijackers, and in doing so had potentially hindered the grand jury's attempts to uncover the truth.
The student's defense attorneys said he was merely confused and paranoid after weeks in solitary confinement.