MENA says the 65-year-old Hisham Barakat died in a Cairo hospital on Monday after undergoing a critical surgery.
He is the top Egyptian official to be assassinated since the ouster of Islamist President Mohammed Morsi two years ago.
Hours earlier, a strong explosion had ripped through Barakat's convoy in the busy upscale eastern suburb of Heliopolis as he was driving to his office in the downtown.
The attack came as Egyptian security forces were already on high alert on the eve of the second anniversary of massive anti-Islamist demonstrations that paved the way, days later, for the military's ouster of Morsi.