Russian Federation leads Group A on goal difference after beating Saudi Arabia 5-0 on Thursday (Friday NZT) in the tournament's first match.
On the other hand, two-time champions Uruguay will appear in their third consecutive World Cup.
But at the Ekaterinburg Arena Suarez proved wasteful.
And El-Shenawy again looked to have preserved a point with a sublime save from Cavani's thunderous volley, before the Uruguay attacker curled a free-kick against the post.
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Which TV channels will broadcast the World Cup Egypt vs Uruguay match?
However, there was a surprising number of empty seats with the attendance being only 27,015. His boss Hector Cuper had confirmed on Thursday that the winger had recovered, tipping him to start but has not made the XI in Yekaterinburg.
Atletico Madrid star José Giménez was the hero as his 90th minute header from a set-piece gave the South Americans all three points.
He added that he appreciated Uruguay as a strong team with some of the best strikers in Cavani and Suarez. Egypt is a slight favorite to go through as runners-up to Uruguay and in front of Russian Federation and Saudi Arabia, but it still won't be easy.
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The Uruguay defender jumped in the area and headed home a free kick late in the 89th minute.
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It came after some horribly slack play from Argentina and was the type of squandered chance teams so often live to regret. Messi was visibly frustrated throughout the match, especially in the moments that followed his missed penalty kick.
Traditional World Cup broadcaster SBS has a much-reduced role at this year's event, further angering fans.
Jose Gimenez has scored in consecutive appearances for Uruguay, also scoring in a friendly against Uzbekistan.
Uruguay had not won their opening match at their last six World Cup tournaments.
How do I watch online live streaming of the World Cup Egypt vs Uruguay match?
In quotes reported on fifa.com, Cuper said: "Mo Salah is an extremely important player for us, nobody can deny that, but you need to have a good team, and we have a good team. He has contributed a great deal to the team and will in future matches".
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