Referee Wilmar Roldan was encouraged to review the decision by VAR, but the Colombian stood by his initial call giving Salam Al Faraj the chance - after a three-minute delay - to drill past El Hadary and pull his side level deep into first-half stoppage time.
No sooner had the veteran goalkeeper finished celebrating and he was facing another spot-kick, this time given after the lightest of shirt tugs by Ali Gabr on Al Muwallad.
Saudi Arabia lost 5-0 in the opening game to Russian Federation but improved their game very much after losing only 1-0 to Uruguay.
"This is football. I apologise to the Egyptian people for our results in the World Cup as well as my teammates in the national team", El-Hadary told beIN Sports.
Salah doing what he does best... scoring lovely goals.
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While Saudi Arabia finish in third place in the group, Egypt end the tournament without a point and have not registered a victory at this competition in seven attempts.
This time, it was Al-Faraj who took on the responsibility and made no mistake in sending El Hadary the wrong way for the equaliser.
With two games played, Saudi Arabia are one of just four teams still without a goal at this World Cup, joined by Morocco, Peru and Costa Rica.
The Liverpool forward put Egypt ahead but wasted a golden opportunity to double the lead, giving Saudi Arabia the chance to claw their way back into the game that was settled by a 95th-minute victor by midfielder Salem Al-Dawsari.
Not bad for the oldest player in World Cup history...
The Egyptian FA confirmed Salah's inclusion in the line-up minutes after a tweet was published with a list omitting the star striker's name. The Pharaohs are taking on Saudi Arabia in a clash that means nothing in terms of progression but has a heavy dose of pride on the line.