Egypt created some decent chances through Mohamed Zidan and Emad Meteb in the first half but that was down to individual efforts rather than teamwork.
Things notably improved after the break, thanks to the substitutions made by coach Shehata.
The best tactical decision was introducing right-winger Ahmed Al-Muhammadi instead of defensive midfielder Hossam Ghaly.
When Al-Muhammadi stepped onto the pitch, Ahmed Fathi moved to the centre of midfield while the former played in his natural position on the wing.
Al-Muhammadi made a significant contribution to Egypt's attacking attempts through his penetration and dangerous crosses while Fathi's work helped midfield become more compact and cohesive after a shaky first-half display.
Ghaly could not showcase his abilities, maybe because he joined up with Egypt late but I believe he will regain top form in the coming games.
The second substitution, which saw Geddo replace Hosni Abd-Rabou, was also crucial.
Although he was playing his first competitive match with Egypt, Ittihad forward Geddo put in a promising display and scored the third goal to wrap up the Pharaohs' win.
This goal, which came against a high-profile team in Nigeria, will surely boost his confidence and help him play the remaining games without pressure.
I'm also very happy that Meteb scored, I already expected that he will be one of the Nations Cup's top scorers.
Meteb played very well in the 2008 tournament despite failing to find the net, dishing out many assists for his teammates. He is one of those players who can convert half-chances.
Mohamed Zidan was also a constant menace to Nigeria's defense through his energetic moves and efficiency in front of goal. He can form a potent partnership with Meteb upfront.
I also have to praise Egypt's captain Ahmed Hassan, who once again proved that the so-called ageing players can perform at the highest level until the end of their careers.
At the age of 35, Hassan perfectly accomplishes attacking and defensive duties without suffering from fatigue.
He sets a great example for young players.
Mohamed Barakat is an Ahli star who won the BBC African Footballer of the Year award in 2005.