In the hard-hitting encounter, the Morocco international, who was brought in as a replacement for Luuk de Jong after 71 minutes, scored the only goal in the game after heading home a cross from Jesus Navas.
Both teams headed for Estadio Ramon Sanchez Pizjuan having emerged victorious in their previous outings.
In the first 45 minutes, the trio of De Jong, Lucas Ocampos and Munir El Haddadi were unable to get the goals as they came up against a solid Levante backline marshalled by Oscar Duarte and Ruben Vezo.
However, the hosts came out stronger in the second half to secure all points at stake despite having manager Julen Lopetegui given his marching orders for a second caution.
El Haddadi put the hosts ahead in the 67th minute but the strike was ruled for offside after VAR replays.
As the game drew to a close, the Frogs began to lose concentration and that gave Sevilla the confidence to attack against Paco Lopez’s side.
Luckily, Los Nervionenses’ never-say-die attitude paid off as En-Nesyri had the final say thanks to his header in the closing seconds of the encounter.
Morocco international goalkeeper Yassine Bounou, who was rarely tested in the game, saw every minute of action, while his compatriot El Haddadi was substituted for Oliver Torres with 20 minutes left to play.
For En-Nesyri, this strike was his first in the 2020-21 campaign. The 23-year-old joined from Leganes last term for a reported €25 million and in his maiden season, he scored four goals in 18 games in the Spanish elite division while playing a role in their Europa Cup triumph.
Thanks to this result, Sevilla have now won both games so far to sit in the fifth position after accruing six points.
Defeat for Levante means they have lost two out of their three games this season and they occupy the 13th spot on La Liga table.