Mohamed Salah did notch his first ever World Cup goal from a VAR-assisted penalty, but the Liverpool forward's deft finish proved a mere consolation for the Egyptians, who now find themselves staring group-stage elimination in the face.
The hosts started with impressive energy and youngster Aleksandr Golovin offered a warning sign for Egypt, taking up space on the edge of the box to whip a curling effort just wide of Mohamed El-Shenawy's goal.
Russia dominated much of the first half but Egypt were able to offer glimmers of quality at times, Trezeguet drifting off the left flank to bend an effort wide of the far post with Igor Akinfeev scrambling.
Cheryshev sought to build from an impressive showing on the opening day of the tournament as he shaped to shoot from the edge of the box, although his speculative effort flew over the crossbar.
Russia made positive inroads down both flanks and Yury Gazinsky soon found space down the left, only to see his eventual cross rise just a matter of inches over the head of Dzyuba.
The returning Salah did not have much to feed off in the first half, but he flirted with glimpses of his best when he got the better of Yuri Zhirkov on the edge of the Russian box. The eventual shot, however, drifted wide before it could test Russian stopper Akinfeev.
The hosts took the lead early in the second half, but it came in bizarre circumstances when Roman Zobnin saw his tame shot deflected off Fathy beyond El-Shenawy in the 47th minute, as the full-back sought to hold off the challenge of Dzyuba.
The opener seemed to kick Russia into life in the final third and they carved out a second after 59 minutes. Right-back Mario Figueira Fernandes produced an adventurous run into the box before cutting a ball back for Cheryshev, who slotted in emphatically.
Egypt were found wanting at the back and Russia added a third three minutes after through the towering Dzyuba, the striker bringing a long ball out of the air, before rounding Fathy and bending a finish into the bottom corner.
An action-packed second period was to continuing delivering too, this time as VAR intervened to hand Salah a penalty after he was brought down inside the area by Zobnin with just over 15 minutes to play. The 26-year-old stepped up coolly to convert from the spot in order to secure his first ever goal at a World Cup.
In the end, however, the response was unable to conjure any sort of comeback for the Egyptians, as Stanislav Cherchesov's charges eased to an emphatic win that now leaves the hosts on the verge of reaching the knockout stages.
RUSSIA (4-2-3-1): Akinfeev; Fernandes, Kutepov, Ignashevich, Zhirkov (Kudryashov 86'); Gazinskiy, Zobnin; Samedov, Golovin, Cheryshev (Kuzyayev 74'); Dzyuba (Smolov 79')
EGYPT (4-2-3-1): Elshenawy; Fathy, Gabr, Hegazy, Abdelshafy; Elneny (Warda 64'), Hamed; Salah, Elsaid, Trezeguet (Sobhi 68'); Mohsen