Substitute Vincent Aboubakar swept in the winner two minutes from time, flicking the ball over defender Ali Gabr and thumping it home.
Nicolas Nkoulou had earlier equalised for Cameroon in the 59th minute, rising highest to power home a header on the hour mark.
The equaliser cancelled out Mohamed Elneny’s opener in the 22nd minute with a beautifully taken near-post strike.
NAN also reports that the victory meant the Indomitable Lions of Cameroon have won the AFCON title for a fifth time.
Egypt who finished as runners up have won a record seven titles with goalkeeper Essam El-Hadary, 44 as the tournament’s oldest ever player.