The emphatic victory ensured the defending champions progressed from Group C as runners-up, finishing behind the Scorchers of Malawi, who claimed top spot in the group.
Egypt started the contest brightly and enjoyed much of the possession in the opening exchanges, moving the ball confidently and looking to unsettle the Nigerian defence. However, despite the early pressure from the Cleopatras, it was the Super Falcons who struck first.
Nigeria broke the deadlock in the 21st minute when experienced striker Asisat Oshoala calmly converted from the penalty spot after Egypt were penalised for a handball inside the area. The goal gave Justine Madugu's side the breakthrough they needed and shifted the momentum in their favour.
The Super Falcons doubled their advantage four minutes before halftime through substitute Monday Gift, who made an immediate impact after being set up brilliantly by Rinsola Babajide.
Egypt refused to go into the break quietly and reduced the deficit in the closing moments of the first half. Nadine Ghazi converted from the penalty spot to make it 2-1 and hand her side renewed belief heading into the interval.
Nigeria, however, returned for the second half with greater intensity and quickly took complete control of the encounter.
Substitute Uchenna Kanu restored the Super Falcons' two-goal cushion after finishing from close range following another well-worked assist from Babajide, whose creativity proved vital throughout the contest.
The defending champions continued to dominate as Christy Ucheibe added a fourth goal in the 81st minute, confidently dispatching another penalty after Nigeria were awarded their second spot-kick of the evening.
Ghazi grabbed her second goal for Egypt with a superb long-range strike that briefly reduced the deficit, but any hopes of a comeback were quickly extinguished.
Late in the game, Michelle Alozie was brought down inside the penalty area, earning Nigeria a third penalty. Captain Rasheedat Ajibade stepped up and calmly converted to extend the lead.
There was still time for another goal as substitute Joy Omewa found the back of the net deep into stoppage time, completing an impressive six-goal performance from the nine-time African champions.
The comprehensive victory underlined Nigeria's attacking quality and depth, with several substitutes making decisive contributions in front of goal.
The Super Falcons will now turn their attention to a highly anticipated quarter-final clash against the Indomitable Lionesses of Cameroon on Sunday, with a place in the semi-finals at stake.