The Super Eagles showed greater composure in the shootout, converting four of their spot-kicks to seal victory.
Egypt faltered from the spot, missing key penalties that ultimately proved decisive.
The match itself was marked by discipline and physical battles, with chances limited at both ends.
Nigeria had a potential breakthrough ruled out earlier in the game, while several yellow cards reflected the intensity of the contest.
Nigeria’s win brings a positive end to their AFCON campaign, finishing on the podium after narrowly missing out on a place in the final.
Egypt, meanwhile, were left to settle for fourth place despite a resilient defensive display.
