A window of the Spanish team's coach was smashed by a crowd of visiting fans as it approached the El Madrigal Stadium. The incident is likely to attract punishment from football's European governing body, UEFA.
A spokeswoman for Villarreal said: "The coach was attacked while the players were aboard and a window was broken. It was a frightening incident, but no-one was hurt."
Fears of trouble in the small town of Vila Real, about 40 miles north of Valencia, had arisen in the days before the match as it was estimated that between 10,000 and 15,000 Rangers fans would arrive, despite an official allocation of only 3,000 tickets. It had also been reported that many of the visitors had forged tickets.
Before the kick-off it was apparent that many Rangers supporters had tickets meant for home supporters. Instead of being penned in their designated separated area, they were to be seen in all four of the stands.
The reported incident came after a day of tension during which eight Rangers fans were detained in Benidorm for hurling bottles and glasses at police.
The eight were arrested for disturbing the peace as a large group of fans prepared to leave the bustling holiday town for Vila Real, further up the coast.