كتب : وكالات
The visitors took an early lead through Larrys Mabiala but the Pharaohs hit back with two-second half goals from Amr Zaki in the 61st minute before the Hodoud midfielder secured the three points.
Egypt are second of Group 12 on three points, trailing Malawi, who thrashed Djibouti 8-1 on Saturday, on goal difference.
Hassan Shehata's men took early control of the game but failed to create any real threat on the Congolese net.
The Pharaohs had the first sight of goal in the 24th minute when Captain Ahmed Hassan struck from the edge of the area but his shot went inches wide.
Emad Meteb missed the target a few minutes later as he failed to convert Hassan's low cross from the six-yard box.
And against the run of play, Mabiala hit a 25-yard free-kick to give his side a stunning opener just two minutes before the break.
A goal down, Shehata had to take maximum risk by using all his attacking options.
Shikabala came in to replace underachieving Hossam Ghaly and Abdul-Malek played for Ahmed Al-Muhamadi.
Abdul-Malek didn't need much time to make an impact as he chipped the ball to Hani Saied, who flicked the ball into the path of Zaki to fire the equalizer from inside the area.
Ahmed Samir Farag limped off the pitch, making way for uncapped Abdul-Aziz Tawfik in the 73rd minute.
Tawfik made a dream start as he fired a powerful long-range drive that was parried by the keeper into Abdul-Malek's path.
From a tight angle, Abdul-Malek curled the ball into the side netting for the winner.
Egypt play Djibouti away on Friday in the second round of the qualifiers.