Police said that Ahmed Javed Khawaja was walking to his clinic in the eastern city of Lahore when he was hit by two shots fired from a motorcycle ridden by two men on Monday.
They said that the early morning shooting prompted protests by several hundred Islamists in the eastern part of Lahore who complained about lack of security, police said.
Khawaja was arrested in late 2002 on suspicion of having links to al-Qaida.
Charges against him were dropped the following year and he was released in June 2003.
Khawaja, who was then 65, was detained on suspicion of assisting some of al-Qaida's most wanted members and illegal possession of weapons.
Among the al-Qaida members he was accused of helping were Yasir al-Jaziri, an Algerian-Moroccan dual national responsible for al-Qaida business, and another figure identified as a close aide to Khalid Shaikh Muhammad, the 11 September mastermind.