In his 10-minute video, Ayman al-Zawahri eulogized Ali Mohammed Abdel-Aziz al-Fakheri, a Libyan militant with the nom de guerre of Ibn al-Shaykh al-Libi.
The militant reportedly hanged himself with bedsheets in his prison cell in Libya in May, according to a newspaper with ties to Libyan leader Moammar Gadhafi's son.
Al-Libi, which means Libyan in Arabic, was captured in Pakistan in 2001 and later sent to Egypt under the CIA's extraordinary rendition program, where he was reportedly tortured and then handed over to Libya.
In the video, Al-Zawahri, dressed in a white traditional Arab robe and white turban, accused President Barack Obama of killing al-Libi and demanded the U.S. "apologize and pay financial and moral compensation" for those who have been detained in secret prisons.
"This is the least to be accepted from you and from your government," al-Zawarhi said, addressing Obama.
Al Qaeda 's no. 2 leader said the U.S. and Arab governments working with Washington tortured al-Libi before eventually handing him over to Libya "to carry on the torture."
Al-Libi was then killed, al-Zawahri said, "on behalf of the American criminal monster, who fools us as the smiling Obama who seeks peace and the defender of human rights."
Many experts believe that Al Qaeda is struggling in the face of Obama's popularity in the Muslim world — especially compared to his predecessor, George W. Bush — and the terror network has frequently sought to portray Obama's policies as a mere extension of Bush's.