Khanfar replaces Adnan al-Sharif, acting manager since June 2003.
Announcing the appointment, Aljazeera Board of Directors pledged continued adherence to its "editorial policy and professional course founded on its ever-present principle of the opinion and other opinion".
Khanfar headed the television channel's Baghdad bureau since the fall of the Saddam Hussein government in April this year. He also previously worked as the channel's southern African correspondent, running its bureau in Johannesburg for several years.
Khanfar's experience as a correspondent extends to conflict areas such as Afghanistan and northern Iraq and India.
Aljazeera Board of Directors expressed its appreciation to al-Sharif for his service and achievements.
Known for its diverse range of discussions, debates and live coverage from several hotspots, Aljazeera TV, with its 30 international bureaus, boasts at least 35 million viewers in the Arab world and elsewhere.