The Liverpool striker, who secured the Pharaohs' opening win with a stoppage-time strike against Zimbabwe on Monday, did it again in Agadir and his penalty before the break is almost certain to secure progression from Group B.
But South Africa should arguably have been given a penalty in stoppage time when Yasser Ibrahim blocked a shot with his arm. After a long delay, the referee decided against awarding the spot kick after consulting video replays and Ibrahim sank to the ground in relief.
Salah converted his penalty after he was struck in the face by the hand of the retreating South Africa forward Lyle Foster. Salah showed no ill effects from the blow and sent his shot straight down the middle while goalkeeper Ronwen Williams dived to his right.
There was still time before the break for Egypt defender Mohamed Hany to get sent off, after receiving a second yellow card for a foul on Teboho Mokoena.
Earlier, Angola and Zimbabwe drew 1-1 in the other group game, a result that suited neither side after opening losses.
Egypt lead with six points from two games followed by South Africa on three with Angola and Zimbabwe on a point each. The top two progress from each group, along with the best third-place finishers.
In Casablanca, Comoros played out a goalless draw with Zambia in the Africa Cup of Nations finals, but the small Indian Ocean island nation came close to an upset win in their Group A clash.
Comoros had the ball in the net in the 19th minute, but Myziane Maolida's attempt was ruled out after a VAR review for a foul in the build-up to the goal.
Maolida had tapped in the ball from close range after a mazy run down the left flank by Rafik Saifi, who played in a pinpoint cross.
But possession was won in a dangerous tackle by Yacine Bourhane on Owen Tembo, and after consulting the sideline VAR screen the referee annulled the goal.
Hosts Morocco were held to a 1-1 draw by Mali also on Friday, ending their world record run of wins and leaving them still to make sure of progress to the next stage.
Midfielder Brahim Diaz tucked away a penalty in stoppage time at the end of the first half but Mali equalised from the spot midway through the second half through Lassine Sinayoko.
Both penalties were awarded after VAR reviews in a tempestuous clash at the end of a busy day of action at the tournament.
Morocco top the Group A standings with four points while Zambia, who they meet next on Monday, have two points along with Mali. The Comoros are bottom of the group on a single point.
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