The African champions capped a fantastic display in the first-half with Mohamed Zidan's strike but they failed to hold on to victory after the restart.
Two goals from Peter Crouch and a third from Shaun Wright-Phillips, both coming off the bench, gave England a morale-boosting win.
Thousands of fans were cheering for Egypt in the 80,000-seater in London.
Hull City striker and Ahli playmaker Amr Zaki took part in the second-half, featuring for the national team for the first time in more than three months.
Explosive Start
Egypt started explosively, with Zidan pulling the strings in the midfield. However, the first chance fell into the path of Frank Lampard.
The Chelsea midfielder was one-on-one with Egypt keeper Essam Al-Hadari but the veteran goalie parried the low shot away.
Minutes later, Zidan connected with a corner-kick and flicked the ball but it was cleared off the line.
Ahmed Al-Muhammadi darted down the right flank more than once and his crosses made troubles for the English defense.
But it was a pass from Hosni Abd-Rabou that created the first goal, sending a long pass towards Zidan, who brilliantly tamed it before smashing past Robert Green.
Lampard had a second golden chance inside the Egyptian area, but his deflected shot went wide.
Fitness Problems
Fitness proved to be the difference between the two sides in the second-half, with England dominating the field starting from the 50th minute.
African Cup of Nations top scorer Geddo was introduced alongside Zaki, but both failed to make an impact.
The Egyptians couldn't defend properly against waves of English attacks led by Steven Gerrard and substitutes Crouch and Wright-Phillips.
Crouch leveled in the 57th minute, poking home from close range after a low cross from Wright-Phillips.
Wright-Phillips turned scorer in the 75th minute when he fired a first-timer on the rebound after Al-Hadari blocked a powerful shot from James Milner.
Hassan Shehata's men collapsed after England went ahead and the third goal was expected soon.
A carbon-copy from England's first, Crouch converted a cross from Wright-Phillips home but the TV replays proved the lanky striker was in an offside position.
The match's goals