A military jury at Guantánamo Bay sentenced two prisoners to 23 years in confinement on Friday for conspiring in the 2002 terrorist bombing that killed 202 people in Bali, Indonesia. But the men could be freed by 2029 under a secret deal and with sentencing credit.

Mohammed Farik Bin Amin and Mohammed Nazir Bin Lep, both Malaysians, have been held by the United States since the summer of 2003, starting with three years in C.I.A. black site prisons where they were tortured. They pleaded guilty to war crimes charges last week.

About a dozen relatives of tourists who were killed in the attacks spent an emotional week at the court and testified to their enduring grief. A jury of five U.S. military officers, assembled to decide a sentence in the 20-to-25-year range, returned 23 years after deliberating for about two hours on Friday.

But, unknown to the jurors, a senior Pentagon official reached a secret agreement over the summer with the defendants that they would be sentenced to at most six more years. In exchange for the reduced sentence, they were required to provide testimony that might be used at the trial of an Indonesian prisoner, known as Hambali, who is accused of being a mastermind of the Bali bombing and other plots as a leader of the Qaeda affiliate group Jemaah Islamiyah.

Then, separately, the judge, Lt. Col. Wesley A. Braun, cut 311 days off Mr. Bin Amin’s sentence and 379 days off Mr. Bin Lep’s because prosecutors missed court deadlines for turning over evidence to defense lawyers as they prepared their case.

But the men could go home earlier. “The pretrial agreement contemplates the possibility of repatriation before the sentence is complete,” said Brian Bouffard, Mr. Bin Lep’s lawyer.

It took so long to get the men to trial, in part, because of the time they spent in the C.I.A.’s secret overseas prison network, where prisoners were tortured during interrogations. Even after they agreed to plead guilty to their crimes and cooperate with prosecutors, the legacy of torture cast a shadow over the proceedings.

Christine A. Funk, a defense lawyer, projected drawings by Mr. Bin Amin of his torture onto a screen in the courtroom as she described him as a broken man who at the time of his capture in Thailand cooperated with the authorities. In addition to his three years in the C.I.A. black sites, she said, he spent his first 10 years at Guantánamo Bay in solitary confinement.

“Upon his arrival in the black sites, he was immediately tortured,” she said. “Not immediately interrogated. Immediately tortured.”

She cited federal and congressional investigations that confirmed he was held naked in isolation while shackled in painful positions, had water poured down his nose and throat, and was forced to squat with a broom behind his knees. Each situation was illustrated by a drawing that is now evidence in the case.

“This is, frankly, un-American,” she said. “This is not who we are. But it is what we did.”

The chief prosecutor, Col. George C. Kraehe, said the true torture victims were the families of the dead, “who have been rendered for their lifetimes horrified, terrorized, bereft of their precious loved ones, stolen from them by the accused’s barbaric acts.”

“Our task here is not to give the accused justice,” Colonel Kraehe said. “Our task here is to give the victims justice.”

He defended the C.I.A. interrogation program as a product of the time, “at the start of the war on terror, when the United States sought to defend itself and the world from forces that had viciously attacked the United States, killing thousands of innocents, forces that had attacked other countries, forces that sought to destroy the American way of life. This war continues to this day.”

Besides, he said, the defendants “left this program approximately 18 years ago.”

Mr. Bin Lep was also tortured, Mr. Bouffard said. But he has decided to forgive those who did it, and move forward.

Both defense and prosecution lawyers gave the jury a lesson in conspiracy as a war crime, and explained that the men became accessories to the Bali bombing by training with Al Qaeda in Afghanistan before the attacks and by helping perpetrators elude capture afterward.

Mr. Bin Lep “may not have planned the bombings, may not have carried them out, may not have known when and where,” Mr. Bouffard said. “But he helped the people who did.”

The chief defense counsel for military commissions, Brig. Gen. Jackie L. Thompson Jr., issued a statement lamenting how long it took to bring the men to trial. He said the U.S. decision after Sept. 11 to establish the C.I.A. interrogation program “frustrated the desire of everyone for accountability and justice.”