The judge, Oscar Magi, said the criminal trial should wait until Italy's highest court ruled whether Milan prosecutors had broken state secrecy rules when pursuing the case, as Romano Prodi's government contends.
The ruling was welcomed by the defence lawyers.
The high-profile case is the first involving the CIA's extrajudicial transfer of terror suspects to third countries.
The trial has been suspended until October 24 and the constitutional court's ruling is expected on October 19.
The ruling will indicate whether the trial will have the power to publicly air details of the US renditions as well as to examine details of what was supposed to be a highly secret operation.
The judge also stopped the clock on the statute of limitations until the trial reconvenes.
The statute of limitations on the charge of abduction with aggravating circumstances is twelve-and-a-half years from the date of the crime; four years and four months have passed so far.
"It's a very clean decision," Alessia Sorgato, a lawyer for several of the US defendants, said.
"It's like sealing the case in Tupperware and putting it in the freezer."
Italian prosecutors say Osama Moustafa Hassan Nasr, also known as Abu Omar, was abducted in an operation coordinated by the CIA and Italian intelligence, then transferred to US bases in Italy and Germany before being moved to Egypt, where he was imprisoned for four years.
Nasr, who was released in February, said he was tortured.
Armando Spataro, a prosecutor, argued the court must continue its deliberations despite the pending case, denying that any state secrets were involved in the preparation of the case and expressing confidence that the decision of the constitutional court would vindicate him.Prosecutors said the decision effectively gives the government inordinate powers to interfere with the justice system.
"Is it possible to have a system in which a trial can be suspended anytime any government decides to launch a conflict?" Ferdinando Pomarici, a co-prosecutor, asked.