Ms Guerin was murdered by a gunman on a motorcycle in Dublin in June 1996 as her car stopped at traffic lights.
John Gilligan, 48, was also cleared of a number of arms charges but was found guilty of having and importing drugs.
The judge said while the court had great suspicions about Mr Gilligan's involvement in the murder, it had not been persuaded beyond reasonable doubt.
Point blank range
Gilligan, who was extradited to Dublin from Britain last February, had denied ordering the murder of Ms Guerin, an investigative reporter for the Sunday Independent.
His lawyers denied he had any active role in running a drugs importation racket that Ms Guerin was investigating.
Two men are already serving life sentences for the murder of Ms Guerin in June 1996.
The journalist was shot six times at point blank range by a gunman riding pillion on a motorbike as she waited at traffic lights in her car at Clondalkin, on the outskirts of Dublin.
Brian Meehan, 36, was convicted in 1999 at the Special Criminal Court in Dublin.
And in 1998 Paul "Hippo" Ward, 35, was found guilty after a trial which showed how he disposed of the gun and motorbike used in the killing.
Ms Guerin had written several exposés of organised crime in Dublin and had been subjected to threats and beatings.
Movie made
A gunman fired through her window in 1994 and she was shot and injured in January 1995 by a masked man who burst into her home.
The mother-of-one had also investigated the IRA, reporting that the group smuggled explosives into Britain and planned a bomb attack in Manchester while it was officially on ceasefire.
Her life-story has already been made into a film - When the Sky Falls, starring Joan Allen, and a new film with the working title of Chasing the Dragon, is planned.
Gilligan's addresses were given in court as Corduff Avenue, Blanchardstown, Dublin, and the Jessbrook Equestrian Centre, Mucklon, Enfield, County Kildare.