Meanwhile, it was a disappointing outing for Cameroon international Allan Nyom who was shown a straight red card for a reckless tackle on Adri Embarba in the 58th minute of the keenly contested tie at the Campo de Futbol de Vallecas.
The West Bromwich Albion loanee who has played 13 matches in the Spanish top-flight this season is now set to serve two-game ban as punishment.
Martin Braithwaite had given Leganes a first half lead in the 36th minute but Nyom's expulsion created a vaccuum in the visitor's defence with Alvaro Garcia converting a rebound to put both sides levelled.
With less than five minutes left before the end of the encounter, En-Nesyri rose highest in Vallecano's penalty area to head Oscar Rodriguez's cross to the back of the net.
The 29-year-old is having a decent debut season with the Cucumber Growers with five goals in 19 LaLiga matches so far this season.
Nigeria defender Kenneth Omeruo was also in action for the entire duration of the game as Leganes climbed four places to 13th spot in the league table.
The Estadio Municipal de Butarque outfit will return to action with a home game against Real Betis on Sunday.