Syrian-born Enaam Arnaout, 41, had pleaded guilty on the eve of trial to conning donors out of as much as $400,000 that went to Muslim fighters in 1990s-era conflicts in Bosnia-Herzogovina and Chechnya, instead of widows and orphans as the charity had advertised.
The US government had hoped for a high profile "terrorism" conviction, but the judge said the case had not been made.
"The government failed to connect the dots...that Mr Arnaout supported terrorist activity," US District Court Judge Suzanne Conlon said in pronouncing a sentence of 11 years, four months.
Arnaout, who is destitute and whose wife and children have returned to her native Saudi Arabia, was also ordered to pay more than $300,000 in restitution to the United Nation's Commission on Refugees.
Not a 'terrorist'
Conlon said Arnaout's personal relationship with al-Qaida leader Usama bin Ladin dated to the 1980s Afghan-Soviet conflict "when this country wasn't necessarily opposed to bin Ladin."
Conlon credited Arnaout for helping raise and distribute roughly $20 million over the past eight or nine years, to help some of the world's neediest people, but he betrayed both the charity's donors and recipients by diverting between $200,000 and $400,000 to purchase such military items as tents, boots and uniforms for Bosnian and, later, Chechen fighters.
"Support of Bosnian and Chechen fighters did not constitute an act of terrorism"
Suzanne Conlon, US District Court Judge
"Support of Bosnian and Chechen fighters did not constitute an act of terrorism," Conlon said.
One of Arnaout's supporters, Caise Hassan, a former board member of the charity, said the judge's sentence was "by the book," but that Arnaout's prosecution was illustrative of the US government's "rounding up of Muslims" in response to the September 11 attacks, which it blamed on al-Qaida.
Prosecutor Patrick Fitzgerald, who has won convictions in the bombings of the World Trade Centre in 1993 and US embassies in East Africa in 1998, charged that Arnaout reneged on a promise to cooperate with investigators after pleading guilty, and that he knew more about al-Qaida's operations than he let on.
In an emotional plea for mercy Arnaout told the judge his life had been "a hell" since government agents raided the charity's suburban Chicago offices and froze its assets in December 2001.
He said he had been held for 15 months in solitary confinement and claimed an FBI interrogator threatened him, saying, "'I'm going to get you, one way or the other.'"
Fitzgerald has said al-Qaida members who have been captured or become informants have painted a picture of bin Ladin, using charities to disguise the network's finances, and he tried to link Arnaout to an effort to collect arms and even uranium for a possible nuclear weapon.
Arnaout's attorney, Joseph Duffy, told the court that the case was unique because of the pressures brought on by the September 11 attacks and that prosecutors had been overzealous.
"The government convicted him before he was found guilty. They labelled him a terrorist," Duffy told the judge during the Arnaout's sentencing hearing. "You would think he was Usama bin Ladin the way they treated him."