However Thomas, a father of three and a former taxi driver, was cleared of two counts of aiding a terrorist organisation.
His wife, mother and father faced the media, after the jury returned from three nights of deliberations to deliver its verdict.
Thomas' father Ian Thomas said he was pleased with the result.
“Jack had nothing to answer for with these charges. We're very pleased with the Jury, we thank the jury and the acquittal has been a great victory,” said Mr Thomas.
The prosecution case relied heavily on a taped interview that Australian Federal Police conducted with Thomas in Pakistan in March 2003.
Prosecutors alleged he attended an al-Qaeda training camp in Afghanistan, and agreed to become a sleeper agent in Australia.
During the interview, Thomas explained why an associate of bin Laden gave him an airline ticket back to Australia.
“He had suggested to me that Osama bin Laden wants an Australian, Aussie, like a white boy to work with him and that there was people in Australia already working for him.”
Thomas’ lawyer Rob Stary said the verdict clearing his client of two counts was a win.
“The fact that Jack Thomas has been acquitted of not supporting a terrorist organisation or being a resource for a terrorist organisation -- which were the two most serious charges in our view -- is a very significant victory.”
Until the jury went out on Thursday Thomas was out on bail.
However he has been in custody since the verdict and will continue to do so until at least Thursday, when Justice Philip Cummins will hear arguments before handing down the sentence.
Thomas faces a maximum 25 years jail on the money charge and two years on the false passport charge.
Mr Stary, said his client would be appealing the conviction on both counts.
No angel
Despite being acquitted of two of the charges, federal Attorney-General Philip Ruddock said Thomas should not be seen as an angel.
Mr Ruddock said to convict people of offences, juries had to be convinced beyond reasonable doubt, and just because that burden was not met, that did not mean Thomas had been victorious.
"Sometimes when people have been committed to trial on the basis that there is sufficient evidence to convict, juries find that on the balance that they have to be satisfied, beyond reasonable doubt that they wouldn't convict, but that should not be seen as somebody who has been convicted of a serious terrorism offence that they are in effect some angel," Mr Ruddock told ABC radio.
"People aren't put to their trial unless a magistrate, in this case a magistrate did judge that there was sufficient evidence to convict on all of the offences, and the fact that the jury comes to a view, that on the test it has to be satisfied beyond all reasonable doubt that they don't convict ought not to be seen as some form of victory," he added.