Chukwueze has been out of action due to thigh injury he suffered in Europa League semi final against Arsenal last season.
The youngster undergo surgery on the injured thigh and he recently returned to full training session earlier this week.
Samuel Chukwueze was introduced to the game on the 76th minute for Arnaut Danjuma, but he was unable to rescue Villarreal from defeat.
Goals from Lucas Torro and Chimy Avila were enough to give Osasuna FC a narrow victory despite the fact that Gerard Moreno netted a goal for the home team.
Villarreal are 11th on the table with 11 points from 12 matches.