The Pentagon said on Wednesday that it had repatriated two Malaysian men from its prison at Guantánamo Bay, Cuba, who admitted to committing war crimes for an affiliate of Al Qaeda that carried out a deadly bombing in Bali, Indonesia, in 2002.

The rare transfer, a day after the Pentagon released another prisoner to the custody of Kenya, reduced the detainee population to 27 men.

The freed prisoners, Mohammed Nazir Bin Lep, 47, and Mohammed Farik Bin Amin, 49, have been held by the United States since 2003. They were returned to the custody of the Malaysian government, and supervision of its de-radicalization program, through a diplomatic arrangement that was reached as part of their guilty pleas in January.

Before they left, the men gave sworn testimony that prosecutors hope will be useful in the eventual trial of Encep Nurjaman, the Indonesian prisoner known as Hambali. Mr. Hambali is accused of being the mastermind of the Bali bombing and other terrorist attacks in 2002 and 2003 as a leader of the Jemaah Islamiyah movement. The men admitted to being accessories to the terror attack, after the fact, by helping Mr. Hambali elude capture.

All three men were held for years after their capture in Thailand in the C.I.A.’s secret prison network that used torture in its interrogations. They were transferred to the military prison in Cuba in 2006, but the military did not formally charge them at the war court until 2021.

Brian Bouffard, a lawyer who represented Mr. Bin Lep at Guantánamo, said his client “plans to live a quiet life with his family. He’s been punished many times over for his long-ago involvement with the wrong people, and we hope one day that his torturers and their enablers might face accountability for the evil they have done in our name.”