Uruguay were far from their best throughout at the Ekeratinburg Arena and it looked as though a series of wasted chances from record-scorer Luis Suarez would prove costly for the Group A favourites.
However, Gimenez's towering late header - which came just moments after Edinson Cavani had hit the post with a free kick - rescued all three points for the South Americans to take them level with hosts Russia at the top of the standings.
The most anticipated team news of the opening round of World Cup fixtures saw Salah only named on the Egypt bench three weeks after damaging his shoulder for Liverpool in the Champions League final, and he stayed there throughout as manager Hector Cuper chose not to risk him.
The Pharaohs fared well without their star player as Uruguay struggled to get into any sort of rhythm in the first half, although they did register the first shot on target after eight minutes when Cavani cut inside before firing a tame low strike into the arms of Mohamed El Shenawy.
It would prove to be a miserable first half for the vaunted front two of Cavani and Suarez, the latter of whom squandered the two best Uruguayan chances of the opening 45 minutes.
The first came at the end of the best passing move from the first half when he got his finish all wrong and skewed an effort well off target, but he left the sparse crowd in the Ekeratinburg stunned midway through the first period with a uncharacteristic miss from close range.
A corner travelled all the way through to the Barcelona striker at the back post, but he scuffed his first-time finish and sent it bobbling into the side-netting with half of the goal gaping.
In the absence of inspiration from the usual Uruguayan suspects, Matias Vecino tried to write the headlines himself with a dipping long-range strike which flew a couple of yards wide shortly before the half-hour mark.
It proved to be the final sight of goal for either side as they struggled to respond to Russia's 5-0 win over Saudi Arabia in the opening match during a lustreless first half, but Uruguay came out quicker in the second half and almost took the lead inside the opening minute.
Again the chance fell to record-scorer Suarez when he latched on to Cavani's lofted ball inside the area, but this time he was thwarted by a big save from El Shenawy, who spread himself to deny the striker from close range.
Uruguay's newfound impetus quickly waned, though, and the match soon fell back into the scrappy and sloppy routine of the first half.
Egypt's first meaningful shot on target did not arrive until the 72nd minute when Ahmed Fathy fired a well-struck first-time effort towards goal from all of 25 yards out, but Fernando Muslera watched it all the way and held on to it comfortably.
The best chances continued to fall the way of Suarez, though, and he continued to waste them. A third gilt-edged opportunity went begging with just over 15 minutes remaining when Cavani flicked the ball into his path, only for Suarez to take too long over his finish and have the ball stolen off his toes by El Shenawy.
The calls for Salah to be handed a brief cameo grew louder heading into the final 10 minutes when Egypt squandered a couple of good chances to break in quick succession, but they were soon ended for good when Cuper made his third and final change.
Uruguay's pressure began to grow in the closing stages and it took a fine one-handed save from El Shenawy to deny a well-struck Cavani volley eight minutes from time, before the late flurry of action which ultimately ended with Oscar Tabarez's side salvaging the win.
Uruguay may well have felt that it wouldn't be their day when Cavani's 88th-minute free kick crashed back off the post with the keeper beaten, and even more so when the rebound fell to Martin Caceres, whose shot into an open goal was inadvertently blocked by his own teammate Carlos Sanchez.
However, Gimenez climbed highest from the corner which followed that scramble, making the ball his and planting a firm header into the corner to send Uruguay's fans and players wild courtesy of their first opening-match win at a World Cup since 1970.
By contrast Egypt were left distraught as their wait for a first-ever World Cup win went on, although Salah will be expected to add more firepower to their attack for upcoming games against Russia and Saudi Arabia.
Uruguay, meanwhile, will face Saudi Arabia in their next group game before taking on hosts Russia on June 25.
EGYPT (4-2-3-1): El Shenawy; Fathy, Gabr, Hegazi, Shafy; Elneny, Hamed (Morsy 50'); Warda (Sobhi 82'), Bekhit, Hassan; Mohsen (Kahraba 63')
URUGUAY (4-4-2): Muslera; Varela, Gimenez, Godin, Caceres; Nandez (Sanchez 58'), Vecino (Torreira 87'), Bentancur, De Arrascaeta (Rodriguez 59'); Suarez, Cavani