Chukwueze started the game on the bench and took the place of Moi Gomez in the 66th minute.
Veteran Spanish midfielder, Santi Carzola put Villarreal ahead from the spot in the 77th minute.
Javi Ontiveros netted the second goal a minute from time with Chukwueze providing the assist.
Chukwueze has so far scored once and recorded an assist in four league appearances for the Yellow Submarines.
Villarreal’s next league game is against Barcelona at the Nou Camp on Tuesday