Two defendants, Saud al-Khalayla and Isam al-Barqawi, were released for lack of evidence, the other 11 received prison terms ranging from six to 15 years for possessing explosives.
The prosecution had accused the 13 men of targeting the US embassy in Amman and military bases near the Iraqi border where US troops are believed to be stationed.
No attacks had been carried out when police uncovered the plot in December 2002, but one of the Jordanian defendants, Zuhair Shudaifat, confessed to planning attacks.
He told military judges that the group sought to "defend Jordan's soil" by purging it of American forces. He was sentenced to a seven-year jail term.
The other nine Jordanians in custody pleaded innocent and said they were coerced into signing confessions.
Al-Barqawi, one of the acquitted, told reporters from the dock that the charges were false and said they were prosecuted because "we have refused to surrender to the policies of Washington and Tel Aviv".
The presiding judge sentenced the alleged "cell leader", schoolteacher Faisal al-Khalidi, to 15 years in jail but quickly commuted it to seven to give al-Khalidi "another chance in life".