Javier Calleja's side waited until after the 90th-minute mark to break the deadlock at the Estadio Ciudad de Valencia and end their three-game winless run in the Spanish top-flight.
Rober's own goal fired the visitors ahead in the 93rd minute before Chukwueze's added his third LaLiga goal of the season three minutes later.
The 19-year-old who was introduced as a 63rd-minute substitute got a pass from Santi Cazorla and impressively curled his left-footed shot past goalkeeper Aitor Fernandez.
.@Eng_Villarreal Nigerian youngster Samuel Chukwueze with his sixth goal of his maiden senior campaign to seal the win vs. Levante.— Tolu Olasoji (@Tollexrism) March 10, 2019
- 3 goals in 16 @LaLigaEN appearances (9 starts)
- 2 goals in 3 Copa Del Rey outings
- 1 goal in 7 @EuropaLeague games (4 starts)
Chukwueze has now scored six goals including an effort in the Uefa Europa League in his maiden senior campaign and has helped Villarreal move to 17th in the league standings with a point above the relegation zone.
As a reward for his impressive showings in the Spanish top-flight, the 2015 Fifa U17 World Cup winner has also been invited for Nigeria's Africa U-23 Cup of Nations qualifiers against Libya on March 20.