Justice Reg Weir, in addition to declaring Sean Hoey not guilty, attacked the prosecution and the police investigation of the case, The Independent reported. He said that police officers lied to make a stronger case and two witnesses were involved in "a deliberate and calculated deception."
The bombing at Omagh in 1998 killed 29 people, many of them women and children. It is believed to have been carried out by an IRA splinter group.
Hoey, 39, an electrician in South Armagh, a heavily Republican area near the border with the Irish Republic, faced 29 counts of murder and other charges. Two suspects are imprisoned in the Republic but have not been tried or convicted.
"I want the world to know that my son Sean Hoey is innocent," Rita Hoey told the BBC. "The authorities north and south have held two separate trials, but one witch-hunt."
Family members of the victims were frustrated by the government's failure to bring the bombers to justice.
"There wasn't an atrocity in the history of the Troubles that more was known about, and yet least was done about," said Michael Gallagher, who lost his son, Aidan.