Two Italians were given three-year prison terms.
Citing diplomatic immunity, Judge Oscar Magi told the Milan courtroom on Wednesday that he was acquitting three other Americans.
Five Italians, including Nicolo Pollari, the former head of Italy's Sismi military intelligence service, and Marco Mancini, his ex-deputy, were acquitted, with Magi saying that the men were protected by state secrecy rules.
Lawyers for the 23 Americans said they would appeal against their convictions.
Ian Kelly, a spokesman for the US state department, said of the judge's decision: "We are disappointed by the verdicts against the Americans and Italians charged in Milan for their alleged involvement in the case involving Egyptian cleric Abu Omar.
"I was brutally tortured and I could hear the screams of others who were tortured too"
Osama Moustafa Hassan Nasr, rendition victim
"The judge has not yet issued a written opinion so we're not in a position to comment further."
George Little, a CIA spokesman, told Al Jazeera that "the CIA has not commented on any of the allegations surrounding Abu Omar".
Al Jazeera's Claudio Lavanga, reporting from Milan, described the verdict as "quite shocking and unexpected".
"I spoke to the prosecutor and he said he was fairly satisfied with the exclusion of Pollari, because he said he wasn't found innocent, but was just not condemned because he was protected by state secrecy," Lavanga said.
"Some of them [those convicted], including Seldon Lady and Jeff Castelli, the CIA chief of station in Rome, left the country when they were found to be part of the operation and they never came back to Italy.
"It is very unlikely they will come now that they have been convicted. The lawyers said that first of all they will appeal, that is a process which can take months.
"And even if the verdict is upheld, it seems unlikely they will be extradited."
Twenty-five CIA agents and a US air force colonel had been cited in the trial, which also involved seven Italian secret service officials.
Abu Omar, an imam granted political asylum in Italy, was taken from a Milan street on February 17, 2003, in an operation allegedly co-ordinated by the CIA and SISMI.
It is alleged that he was then taken to a US air force base in northeastern Italy, then flown to the US base in Ramstein, Germany, and on to Cairo.
He was released after four years in prison without being charged, and currently lives in Egypt.
Abu Omar told Human Rights Watch in 2007 that he was "hung up like a slaughtered sheep and given electrical shocks" during his time in Egypt.
"I was brutally tortured and I could hear the screams of others who were tortured too," he told the organisation.
His suspected captors failed to take many standard precautions and had spoken openly on mobile phones, leaving investigators to suspect that the US agents had cleared their intentions with senior Italian intelligence officials.
Abu Omar's lawyer is requesting $14m in damages.