BBC correspondent Steve Swann observed the trial and relayed that there was little evidence tying Abu Qatada to the plot. A co-defendant's confession that implicated Abu Qatada could not be corroborated.
Abu Qatada will remain in custody to face an additional charge of attempting to bomb millennium celebrations in Jordan. That trial is expected to begin in September.
Abu Qatada, whose real name is Omar Othman, was extradited to Jordan from Britain in July 2013 after a lengthy legal dispute that began in 2005.
Britain's Home Office minister James Brokenshire commented on Thursday's ruling:
"Abu Qatada's re-trial in Jordan has been made possible thanks to this government's determination to successfully deport him from the UK.
"While the courts in Jordan have acquitted [Abu] Qatada of one of the two charges against him, it is right the due process of law is allowed to take place in his own country. We await a verdict on the remaining charge."
Abu Qatada cried in court when he learned he had been acquitted.
If released, a deportation order will not permit him to return to the U.K., and a U.N. travel ban will remain in effect.