El Hadary, who has just turned 44, came off the bench in Tuesday's 0-0 draw with Mali when El Shenawy hurt himself.
In doing so he beat the age record of 39-year-old compatriot Hossam Hassan.
BBC Sport has learned El Shenawy is out of the finals with a hamstring tear and Ekramy is being treated for a hamstring strain, leaving Egypt with no back-up.
Ekramy suffered his injury during training on 14 January and is undergoing intensive treatment in the hope he can recover to play if required.
Despite the critical situation, BBC Sport has been told the Egyptian Football Association will not seek to call up another goalkeeper to the squad because it believes it is not permitted under the Confederation of African Football's tournament regulations.
Caf's rules state that a replacement player cannot be called up later than 24 hours before a team's opening game of the tournament.

Jodie Wilkinson, 27, was attacked by a group of up to 11 men in Stanhope Street, Newcastle, on 11 October.
Sharif Kalimba, 19, of no fixed address, has been charged with violent disorder and remanded in custody.
Four men from Newcastle, aged 25, 25, 22 and 20, have been charged with violent disorder. David Waterston, 43, from the city, was charged with murder.
Mr Kalimba is due to appear at South East Northumberland Magistrates' Court on Monday.

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Haskins was awarded the belt after Randy Caballero was stripped of his title after weighing in five and a half pounds over the limit for last Saturday's fight, which had been due to take place at the Mandalay Bay Hotel.
Bristol-based manager, Chris Sanigar, told BBC Points West about his future hopes for 32-year-old Haskins.

Joedyn Luben, 32, had £77,000 in a safe at his home in Penlan, Swansea, he told Cardiff Crown Court.
He claims officers from South Wales Police stole £30,000 of this during the raid in April 2011.
Det Sgt Stephen Phillips, 47, of Swansea, Det Cons Christopher Evans, 38, of Llangennech, and Michael Stokes, 35, from Glynneath, deny theft.
Mr Luben told the court on Tuesday he gave the code to the safe to Det Con Stokes when asked by the officers.
He said he had been saving the money since he was 16 and last used the safe the night before the raid, when he deposited £12,000 following the sale of a car.
No action was taken against Mr Luben so a cheque was written for him to return his money.
However, he said this was £30,000 short of what was seized.
The case continues.

One sign depicted a woman above the word "kitchen" and another showed a man alongside the word "stadium".
Lyon's president said on Twitter the club were investigating the incident.
Lille have since confirmed their home match against Lorient on Saturday will be free for all women, saying: "Ladies, you are welcome with us."
Lyon's women's team have won the French title 14 times and their captain Wendie Renard highlighted the banners on Twitter, saying: "Lyon supporters... can you give me an explanation for that banner? The men at the stadium, the women in the kitchen?"
Club president Jean Michel Aulas replied: "The club will get tough and will file a complaint against the creator of this banner."
Lyon, who are fourth in the league, lost the match 2-1 at Parc Olympique Lyonnais.
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14 May 2016 Last updated at 18:29 BST
Ahmed Soultan, a pioneer of Morocco's urban music scene,
Listen to a sample of his track Afrobian which features Femi Kuti, Fred Wesley and Pee Wee Ellis.
The oldest Africa Cup of Nations player Essam El Hadary is Egypt's only fit goalkeeper in Gabon after injuries to Ahmed El Shenawy and Sherif Ekramy.
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A further man has been charged in connection with the fatal stabbing of a woman, bringing the total to six.
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Britain's Lee Haskins could return to Las Vegas for a big pay day after winning the IBF world bantamweight title without throwing a punch.
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Three detectives stole a man's life savings in a raid on his home, a court has heard.
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Lille have offered free entry to women after sexist banners appeared in the home crowd in Saturday's Ligue 1 match at Lyon.
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DJ Rita Ray looks at some of the best recent music releases from Morocco - and why some North African musicians are seeking inspiration further south.