The CIA's former station chief in Milan, Bob Seldon Lady, was convicted in absentia along with 22 other agents in 2009 by Italian authorities, over the kidnapping of Osama Mustafa Hassan Nasr, better known as Abu Omar.
The cleric was taken to the Aviano US air base in northeast Italy, flown to a US base in Germany, and on to Cairo, where he says he was tortured.
Lady received the heaviest sentence, which was increased from eight to nine years on appeal in 2010, though he was never extradited and never served any of his term.
Under the programme, suspects were sent to countries where they are detained, interrogated and possibly subjected to ill-treatment.
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Lady, "who was sentenced to nine years in prison, has received a partial pardon of two years," a statement from the Italian presidency said yesterday.
Betnie Medero, also a CIA agent, was granted a similar pardon, the statement said.
The decision to reduce the sentences was based on the United States' suspension of the extraordinary rendition programme since President Barack Obama first assumed office in 2009, it added.