According to officials, Auj was shot three times in the neck as he was heading to Korangi to attend an event with a fellow professor in his vehicle, Dawn online reported.
Auj died on arrival at the Aga Khan University Hospital.
Auj was an author, professor and dean at Karachi University's faculty of Islamic studies.
He also edited Al-Tafseer, a research journal on Islamic studies.
He was associated with the university for 19 years and headed the Islamic studies department since Feb 1, 2012.
Karachi police have launched a probe into the killing.