The slim 1-0 win over the Afcon hosts came at a time when many had lost hope in Bafana Bafana following a disappointing group-stage campaign.
The Pharaohs had dominated Group A, but they were stunned by the underdogs Bafana, who snuck into the Round of 16 as one of the four best third-placed teams.
Man of the match Thembinkosi Lorch's solitary strike earned the 1996 Afcon champions a place in the quarter-finals and set up a date with the Super Eagles of Nigeria.
The performance has prompted hope that Bafana are peaking at just the right time.
Poor preparations had a negative impact on Stuart Baxter's side as they did not play any full friendly matches ahead of Africa's most prestigious tournament - a factor which head coach Baxter alluded to after the Egypt game.
South Africa had only one 'fixture' which was a mere training game against Ghana's Black Stars, and ended in a goalless stalemate.
Angola then pulled out of their planned friendly match against Bafana at the last minute despite the expectation being that it would have been South Africa's last warm-up game before they embarked on their Group D campaign.
This saw the South African Football Association's plans come under scrutiny from fans and media alike.
Nevertheless, the team produced lacklustre performances in the group stage which saw them lose to both Ivory Coast and Morocco - failing to register a single shot on target. Even their win over neighbours Namibia did little to convince their detractors.
However, it turns out that Bafana used their group stage matches as preparation for the 'business round', the knockout phase, because there was improvement and they looked organised and bold against the Pharaohs.
Experienced defensive midfielder Dean Furman led by example, and his return from injury proved to be a massive boost as he produced a superb display just in front of the Bafana defence.
In addition, the reigning PSL Footballer of the Year Lorch shone brightly in attack in his first appearance in the tournament, and combined very well with Percy Tau and Lebogang Mothiba as the front three.
If Baxter's charges can show a similar desire and play this way against Nigeria, they could stun the three-time champions.
However, South Africa must demonstrate that the Egypt victory was evidence of the belated preparation paying off, and must silence any concerns that they've peaked too soon.