Talae El-Gaish midfielder Mohamed Shehata scored the winner with a powerful shot from outside the area after just eight minutes.
Despite several threats from Guinea, including two saves by Egypt's keeper Hamza Alaa and a missed chance by a Guinean striker, the young Pharaohs held on to their lead.
Egypt will now face the winner of the other semi-final between hosts Morocco and Mali in the final on Saturday.
The top three teams from the tournament qualify directly for the Paris Olympics, while the fourth-placed team will enter a playoff round.
Egypt skipper Ibrahim Adel had a chance to double the lead just before the break, but he failed to control the ball from close range.
In the second half, Guinea intensified their attack to level the score, but Alaa and his backline foiled all their attempts.
Defender Hossam Abdel-Meguid appeared to add a second goal for Egypt in the 71st minute, but the goal was disallowed after a VAR check for offside.
Despite a difficult final stretch, Egypt held on to their lead and secured their ticket to Paris 2024.
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