However, the Saudis were level just moments later when they were awarded a second spot-kick, after Ali Gabrin was adjudged to have pushed Al Muwallad in the box.
Saudi Arabia were awarded a second penalty on the stroke of half-time, although there was a change in the penalty-taking duties as Salman Al Faraj took responsibility and scored.
At 45 years and 161 days, El-Hadary is making his 153rd appearance for Egypt, and he's the oldest player to ever play in the World Cup.
The win, settled by midfielder Salem Al-Dawsari's angled strike in the 95th minute, meant Saudi Arabia finished third in Group A, scoring their only goals in Russian Federation and putting behind them an opening day 5-0 thrashing by the hosts.
Saudi Arabia were thumped 5-0 by Russian Federation and then lost 1-0 to an unconvincing Uruguay.
NAIJ.com previously reported that Uruguay left it late to secure a vital 1-0 victory against Egypt as day two of the World Cup got underway at the Ekaterinburg Arena on Friday, June 15.
Saudi Arabia had earlier gone 11 matches without recording a win at a World Cup.
Saudi Arabia finished Group A in third place with three points, while Egypt was last after losing all three of its games.
Liverpool superstar Mohamed Salah opened scoring for the north African outfit in the 22nd minute with an assist from Abdalla El Said.
Egyptians, however, rejoiced when Mohamed Salah landed a penalty shot that was successfully scored as Egypt's first World Cup goal since 1990.
El-Hadary pulled off a stunning stop, making him the oldest goalkeeper to save a penalty at the tournament.
It was an opening half of record achievements and firsts.