Spartak were ordered to play two home games behind closed doors, the second being a normally mouth-watering fixture against Zenit next weekend, after their fans rioted during a 1-0 cup win at second division Shinnik Yaroslavl on Wednesday.
Lokomotiv's win left them on 33 points from 15 games, three less than Zenit who were held to a 1-1 home draw by seventh-placed Amkar Perm on Saturday, and three ahead of third-placed Spartak.
N'Doye fired Lokomotiv ahead with a clinical finish in the seventh minute after midfielder Dmitri Tarasov found Maicon with a long ball and the Brazilian squared it for his strike partner, who blasted his shot from eight metres into the roof of the net.
Rattled by the opener, Spartak soon found themselves two goals behind after a howler by goalkeeper Sergei Pesyakov, who let an innocuous long ball bounce under his body and fall perfectly for Alexandr Samedov to steer it into an empty net.
The home side pulled one back in the 27th minute after Armenia striker Yura Movsisyan beat Lokomotiv keeper Ilya Abaev to an inviting Sergei Parshivlyuk cross from the right and poked it in from close range.
Pesyakov made some amends for his error with two good saves shortly before halftime to keep Spartak afloat, but was powerless in the 78th minute when N'Doye made his size and physical strength count.
With instructions from both benches echoing in the eerily empty stadium, the robust striker took a long crossfield pass by Vitaliy Denisov into his stride, shook off his marker with some ease and drilled an unstoppable shot from 13 metres past Pesyakov.
(Writing by Zoran Milosavljevic in Belgrade; Editing by Pritha Sarkar)
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