The 19-year-old’s effort proved decisive to help Javier Calleja’s men end a four-game winless run at Estadi Montilivi following defeat to Celta Vigo, a draw with Barcelona and back-to-back losses to Real Betis and Valencia.
With only seven minutes into the encounter, the youngster found the back of the net after he was set up by Pablo Fornals to take his tally to eight goals in all competitions this season.
Despite efforts from Eusebio Sacristan’s men to equalise, the Yellow Submarine held onto the first-half lead to claim their seventh win of the season.
Chukwueze featured for 76 minutes before he was replaced by Alfonso Pedraza while Cameroon international Karl Toko Ekambi made way for Santiago Caseres in the 57th minute.
The win saw Villarreal move up to 15th place in the log after gathering 33 points from 32 games.
They will now shift their focus to the second leg of their Europa League quarter-final game with Valencia on Thursday.