The release had been ordered by President Hamid Karzai several weeks ago, after his government took over the prison from US troops.
The decision had prompted angry denunciations from Washington and strained relations between the two countries ahead of the year-end withdrawal of most international combat troops US forces in Afghanistan say the men have the blood of international and Afghan soldiers on their hands.
They boarded a bus to leave the facility, laughing and smiling, he said.
The US has argued for the detainees to face trial in Afghan courts, citing strong evidence against them, from DNA linking them to roadside bombs to explosive residue on their clothing, but Kabul has cited insufficient proof to hold them.
Karzai, too, has referred to the Parwan prison as a "Taliban-producing factory" where innocent Afghans are tortured into hating their country.
Among those who were expected to walk free today are Mohammad Wali, who the US military says is a suspected Taliban explosives expert who allegedly placed roadside bombs targeting Afghan and international forces.
The military said Wali had been biometrically linked to two roadside explosions and had a latent fingerprint match on another improvised explosive device, as well as testing positive for explosives residue.
The US military had formally disputed the prisoners' release, but an Afghan review board had effectively overruled those challenges.
The detainees' release has been in the works for weeks, and comes as Karzai's government has taken an increasingly hostile tone toward the US ahead of the withdrawal of NATO combat troops at the end of 2014.
