The action was brought to a halt just minutes before the final whistle as gas engulfed the pitch at El Madrigal, before the players eventually returned and the match was completed.
With the game just minutes from the final whistle and Celta leading 1-0, the pitch at El Madrigal was engulfed as a smoke bomb landed close to the visitors' goal.
Fans left the stadium, many covering their faces to protect themselves, while the players returned to the dressing rooms.
The match eventually got started again and Nolito scored a second for Celta to give the Galicians a valuable 2-0 victory.
"Villarreal absolutely condemns this behavior," club president Fernando Roig said afterwards. "It has obviously come from someone who wanted to harm our club.
"We have all suffered the consequences of this, but it was obviously planned - it came from the area where our quietest fans [are seated]."
The incident comes only a few days after Cristiano Ronaldo was struck by a lighter thrown from the stands in the derby between Atletico and Real Madrid at the Vicente Calderon on Tuesday.