Edinson Cavani rounded off a third successive victory for the South Americans, who finish the first phase with a 100% record and are yet to concede a goal.
The hosts had exceeded expectations to convincingly beat Saudi Arabia and Egypt but their bubble started to burst only 10 minutes into their final group game.
Suarez slotted a 20-yard free kick into the bottom corner, after defender Sergei Ignashevich had made the target bigger for him by abandoning his position at the end of the wall.
Stanislav Cherchesov's side had responded well but found themselves with a mountain to climb when Diego Laxalt's hopeful shot took a massive deflection off Cheryshev, and beat Igor Akinfeev's despairing dive into the bottom corner.
A comeback was made nigh-on impossible when two reckless challenges from Smolnikov, only called into the team to give Mario Fernandes a rest at right-back, in the space of 10 minutes saw him dismissed with nine minutes of the first half still to go.
Although they held their own for much of the second period, Russia barely created anything that would trouble Uruguay goalkeeper Muslera on his 100th international cap.
Three-goal top scorer Cheryshev was sacrificed after the red card and target man Dzyuba, who had bullied his way to a couple of goals in the tournament thus far, found an equal in Uruguay captain Diego Godin.
Dzyuba did have one opportunity to set up an exciting finish on 74 minutes when Russia pinched possession in the final third, but the 6ft 5in striker could not bend his shot inside the post after checking back onto his left foot.
Sitting safely on their seventh successive clean sheet, Uruguay pushed for a third late on but Cavani's attempts to get on the scoresheet were initially fruitless, slicing a 20-yard shot horribly wide from a chance he created himself.
Suarez should have teed his strike partner up for a simple tap-in only to overhit a square pass, but Cavani eventually got his first goal of the tournament when he poked home the rebound of Godin's header in the 90th minute.
Uruguay and Russia now wait to discover their last-16 opponents as Spain, Portugal and Iran vye to qualify from Group B tonight.
URUGUAY (3-5-2): Muslera; Caceres, Coates, Godin; Laxalt, Nandez (Rodriguez, 73'), Torreira, Vecino, Bentancur (De Arrascaeta, 63'); Suarez, Cavani (Gomez, 90')
RUSSIA (4-2-3-1): Akinfeev; Smolnikov, Kutepov, Ignashevich, Kurdjasov; Samedov, Gazinskiy (Kuzyayev, 46'); Miranchuk (Smolov, 60'), Zobnin, Cheryshev (Fernandes, 38'); Dzyuba