Two goals from Zamalek left-back Ahmed Fatouh and Galatasaray striker Mostafa Mohamed late in the first half gave Egypt a comfortable advantage after a cagey opening.
Pyramids FC winger Ramadan Sobhi came off the bench to put the icing on the cake with a third goal on 71 minutes as Egypt put in an even better display than the one they produced in Friday's 1-0 home win over their North African neighbours.
Egypt top Group F with 10 points, four ahead of Libya with only two matches remaining. Gabon are third on four points, with Angola lying at the bottom on three.
The Pharaohs need just a win from their final two games against Angola and Gabon next month to ensure they would finish on top and reach the final two-legged playoff for a place in next year's World Cup finals in Qatar.
Egypt dominated from the outset, although the artificial turf at the 28 March Stadium in Benghazi made it difficult for both sides to move the ball around.
The visitors pressed Libya high up the pitch but it took them 21 minutes to create their first chance when Stuttgart's on-loan winger Omar Marmoush, scorer of the winner on Friday, latched onto a through pass from Fatouh and rounded the advancing keeper, only to miss the target from a tight angle.
Egypt made an unscripted substitution shortly after when towering goalkeeper Mohamed El-Shennawi picked up a hamstring injury, making way for Zamalek's Mohamed Abou-Gabal.
Television cameras caught El-Shennawi arguing with Essam El-Hadary, Egypt's iconic shot-stopper and the current goalkeeping coach, on his way out. The Ahly goalie was apparently dismayed by the decision to field him while he is not fully fit.
Mohamed sent a weak shot into the keeper's hands when well positioned to score but made amends on 39 minutes to help Egypt break the deadlock.
He superbly controlled a flick from Mohamed Salah with his back to goal on the edge of the area and, although he failed to keep his balance, he released Fatouh with a sliding pass to fire an angled low shot into the bottom corner with his first touch.
Mohamed then turned scorer on the stroke of halftime for only his second international goal, meeting an inviting cross from Marmoush with a superb far-post header that nestled into the opposite corner of the net.
Egypt eased off after the break, allowing Libya to pile on pressure that resulted in two decent efforts, including a shot from winger Hamdou Elhouni that Abou-Gabal did well to smother at his near post.
But Sobhi ended the match as a contest in the 71st minute when he ran onto a defence-splitting pass from Salah, who otherwise had a subdued game, to send a delicate shot into the far bottom corner from close range.
It was his second international goal and first since March 2016, when he struck in an African Cup of Nations qualifier against Nigeria when he was only 18 years.
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