Ridha Ahmad al-Najjar and Lutfi al-Arabi al-Gharisi were flown home on June 15, officials said.
Both men had been incarcerated by the Afghan regime since December, when the United States handed over control of prison operations in Afghanistan under a bilateral security treaty.
"The Defense Department transported two Tunisian males in Afghan custody to Tunisia in support of the government of Afghanistan," Pentagon spokesman said Lieutenant Colonel Myles Caggins said.
Najjar, whom the CIA suspected of having been Osama bin Laden's bodyguard, was captured in May 2002 in Karachi and became the first prisoner of the CIA's notorious "Salt Pit" prison in Afghanistan that has since closed.
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According to the Senate report on the CIA's detention program, Najjar was held by the intelligence agency for over 700 days.
He was left hanging from handcuffs and forced to wear a diaper for more than 22 hours a day, two days in a row, to "break his resistance."
According to the same report, CIA interrogators described Najjar as "clearly a broken man" who was "on the verge of complete breakdown" after he was placed in isolation.
He even "became the model" for other detainee interrogations.
Less is known about Gharisi. The Senate report states only that he had also suffered "enhanced interrogation techniques" during his 380 days of CIA incarceration, and endured at least 48 hours of sleep deprivation in October 2002.
President Barack Obama has called the CIA's enhanced interrogation techniques torture.
Most prisoners of war captured by the United States in Afghanistan were detained at Bagram prison near Kabul.