The result completed a perfect week for Pitso Mosimane's side, who had beaten Eritrea 5-0 in their AFCON 2027 qualifier on Wednesday.
Mosimane made nine changes to the team that started against Eritrea, with only Ime Okon and Sphephelo Sithole retaining their places. Debutants Dithejane and Tashreeq Matthews were handed starting roles, while Luther Singh was also included after scoring as a substitute in the midweek victory.
Cassius Mailula led the attack, with Brooklyn Poggenpoel partnering Sithole in midfield. Sipho Chaine captained the side, while Lebone Seema, Thabang Matuludi and Fawaaz Basadien completed a youthful-looking defence.
Egypt, meanwhile, made only three changes from the side that had defeated South Sudan 5-0.
The hosts threatened early, with Omar Marmoush cutting inside Okon before curling an effort wide in the ninth minute. Four minutes later, Okon's headed clearance fell kindly for Mohamed Hany, but the Egypt full-back fired over.
South Africa gradually settled into the contest, with Matuludi offering an attacking outlet from right-back. He fired wide after combining with Matthews before testing Shobeir again with a better effort shortly before half-time.
Dithejane also came into the game as the half progressed and created an opportunity for Mailula, whose effort was comfortably dealt with by Shobeir.
Seema was another standout performer for Bafana, producing a series of important clearances and a crucial block to keep the hosts at bay.
South Africa eventually broke the deadlock five minutes into the second half.
Shandre Campbell, introduced at the interval for Singh, sent a ball forward which prompted Shobeir to rush from his goal. Dithejane pressured the goalkeeper into a poor clearance, which struck the Bafana debutant and fell kindly into his path.
With the goal at his mercy, Dithejane kept his composure to finish into an empty net and give South Africa the lead.
Mosimane subsequently brought Ricardo Goss on for Chaine, and the Sundowns goalkeeper played an important role in protecting the advantage.
Goss produced an excellent save to deny substitute Hamza Abdelkarim before making another crucial intervention in stoppage time, diving low to keep out Ibrahim Adel's header.
Abdelkarim struck the crossbar with the rebound, but Bafana held on to complete an impressive victory against a much more experienced Egypt side.
The win also provided Mosimane with another positive result in his return to the Bafana dugout, while Dithejane's debut goal gave the coach another attacking option to consider.