An own-goal from former Ismaili defender Dario Khan and a superb strike from the on-fire Mohamed Nagi 'Geddo' sealed the victory for the defending champs.
The six-time African champions set a new record of 15 unbeaten matches in a row, surpassing Cameroon's previous run in the 80s.
Egypt are guaranteed top spot in Group C with six points from two games, while Mozambique are bottom with a single point.
Hassan Shehata replaced holding midfielder Hossam Ghaly with playmaker Shikabala to increase firepower, while no other changes have been made to the side that beat Nigeria.
Even First Half
Surprisingly, the opening half-hour was evenly-balanced, with Mozambique looking more organized than their high-profile opponents.
Egypt's first shot on target came in the 25th minute when Shikabala's low effort forced a good save from Mozambique keeper Rafael Kapango.
Three minutes later, Shikabala drilled in an inviting ball that beat the keeper, but found no player with a red shirt to tap in.
Despite the slight liveliness, Mozambique's basketball-style defense kept on denying Egypt any space in the final third.
The best chance of the half though came in the 48th minute when the Egypt-based Kapango thwarted Emad Meteb's powerful shot from 18 yards.
Early Favor and Geddo Magic
Egypt started the second half with a flyer when Ahmed Fathi's powerful cross was deflected by Khan into his own net two minutes after the break, with the latter scoring his second own-goal of the tournament.
Shehata immediately brought on attacking winger Ahmed Al-Mohammadi for Hani Saied in an attempt to fortify the lead.
But despite the early goal and the offensive substitution, Egypt still looked nowhere near their coherent performance against Nigeria in the first game.
Shehata tried more options upfront as Ahmed Eid came on for the ineffective Mohamed Zidan, who was far from satisfied to be off, before Geddo replaced Shikabala.
It was Geddo who added some glamour to the victory, maintaining the staggering start to his international career with a third goal in as many games.
The Ittihad forward received the ball from Ahmed Hassan with his back to goal, turned it to his left foot and smashed in a spectacular volley into the top-left corner nine minutes from the end.