It was a far from impressive performance from the Egyptians but a rare attack near the end of the match gave Nagui his fifth goal of the tournament and snatched a record seventh African championship for his country.
He curled a shot into the Ghana net from a tight angle after a smart one-two with striker Mohamed Zidan, who had been largely anonymous throughout the game.
"We have achieved what no other side has ever done. This is the best team ever in the history (of African football)," said victorious coach Hassan Shehata.
Ghana, badly affected by injury to key players, had surprised many with their progress to the final but despite an inexperienced line-up they took the game to their opponents.
Egypt, who missed out on qualification for this year´s World Cup finals, started with nine of their winning team from two years ago while only two of Ghana´s side had been born when they last won the Nations Cup in 1982.
"We won this to make up for the disappointment of the World Cup," defender Wael Gomaa told a news conference.
CAGEY GAME
Ghana created more of the limited chances in a cagey game, devoid of any tempo and pace in the muggy and humid conditions in the Angolan capital.
Striker Asamoah Gyan, who played a lone role up front, was full of enterprise and came close with several efforts, all of them from outside the box.
Most of the goal-bound efforts came from long range as both defences held tight for much of the game and players retreated quickly behind the ball when without possession.
Egypt had two opportunities midway through the second half but both Emad Moteab and Zidan were let down by their first touch.
Ghana might have forced the game into extra time with the last attack of the match after a cross from Samuel Inkoom evaded the Egypt defence but fell wide off the chest of substitute Eric Addo.
The win meant Egypt extended their run of unbeaten games at the Nations Cup to 19.
Captain Ahmed Hassan, named man of the match, became the first player to win four Nations Cup medals.
