Joanna Hawkins, an army spokesperson, said the military court at Fort Meade, Maryland, just outside Washington, convicted Jordan of willfully disobeying a superior commissioned officer.
But Jordan was acquitted of being responsible for cruel treatment of detainees.
Prosecutors said Jordan was in charge of an interrogation centre at the prison west of Baghdad, but his defence team said he had no command authority over anyone there.
Jordan was expected to be sentenced later on Tuesday and could face a maximum penalty of five years in jail and dismissal from the army, Hawkins said.
Images of the 2003 abuse, including naked detainees stacked in a pyramid and others cowering before snarling dogs, became public in April 2004.
The widely publicised pictures triggered international condemnation of the US and damaged the reputation of the US military as it waged war in Iraq.
Several low-ranking soldiers have been convicted in military courts in connection with abuse within Abu Ghraib prison.
Two officers senior to Jordan at Abu Ghraib have been disciplined by the army but neither have faced criminal charges.