The Russian covered the distance in 32: 11.1.
Another representative of Russia, Artyom Maltsev, finished second, and Frenchman Maurice Manifika closed the top three.
Another Russian, Denis Spitsov, took fourth place.
His compatriot Ivan Yakimushkin finished after him.
Earlier it was reported that Nepryaeva and Stupak would not be suspended for violating the mask regime at the Tour de Ski.