After a dim start to the first half, the Uruguayans had the first sight at goal after Martin Caceres broke out wide and played in a cross for Edinson Cavani, who failed to convert on 12 minutes.
Cavani's partner-in-crime Luis Suarez had a chance of his own minutes later after being played in behind the defence, but he only found the side-netting.
The South Americans broke the deadlock on 22 minutes through Suarez, who guided the ball home from a corner kick.
Regardless of the lead, the openings still fell for the Saudis and the best one came on 28 minutes from a cross on the left but striker Hatan Babhr was unable to keep his effort down as he skied over the top.
Saudi Arabia were dealt a blow just before half-time as Hussain Almoqahwi replaced the injured Taiseer Aljassam following a coming-together with Suarez.
Apart from a Suarez shot getting palmed away following a free-kick, the Uruguayans were left dwindling for most of the opening 15 minutes of the second half.
Lucas Torreira's impact off the bench for Uruguay was almost immediate as his cross-cum-shot took a deflection and sailed inches wide of the mark.
In the 85th minute, Cavani squandered a chance to get his first 2018 World Cup goal when he shot straight at goalkeeper Mohammed Al Owais after being sent through one-on-one.
The Uruguayans held on in the last few minutes and joined host nation Russia in the knockout stages, while Egypt and Saudi Arabia were eliminated.