The Nigeria wideman finished calmly with his left foot from close range in the 75th minute after a superb pass by Juame Costa, who had been played in through a fine ball over the top by Manu Trigueros.
The winger was replaced by Gerard Moreno two minutes after opening the scoring, as Unai Emery looked to rest some of his stars ahead of the visit of Elche on Sunday.
The win guarantees Villarreal’s place in the Europa League knockout stages, as they extend their advantage at the top of Group I.
Max Gradel, Isaac Coffie, Faycal Fajr, Samba Camara, Mamadou Samassa, Arouna Kone, Aaron Appindangoye, Casimir Ninga and Mustapha Yatabare all featured for a Sivasspor team heavily dominated by African talent.
The Spaniards have 13 points after five games, and remain unbeaten in their group stage campaign, having won four of their five matches to date.
In the group’s other fixture, Maccabi Tel Aviv remain in second place in the group after drawing 1-1 at already-eliminated Qarabag FK of Azerbaijan.
The win extends the Yellow Submarine’s superb run of form both domestically and in Europe, as they have now gone 14 matches without defeat in all competitions, winning nine matches since their last defeat—a 4-0 humbling by Barcelona in late September.
For Chukwueze, the goal will prompt some optimism that he finally answer the accusations of inconsistency that have been levelled at him in recent years.
The Nigeria international had a hand in three goals in three games at the end of October and early November, scoring against Real Valladolid and Sierra Leone after contributing an assist against Qarabag.
However, he didn’t weigh in with goals in his next four matches after the 4-4 draw with Sierra Leone for the Super Eagles, having not contributed a goal in the previous six fixtures before the 3-1 victory at Qarabag.
Chukwueze has scored one and contributed another assist in 10 La Liga appearances so far this season, but will need to improve dramatically if he’s to increase his return of last season—three goals and two assists in 37 league outings.
Last term his numbers were down on the season before, when he scored five and weighed in with two assists in 26 outings for the Yellow Submarine.