Luis Suarez and Neymar lie on the turf after being struck by objects
Image credit: Reuters
Messi scored a late penalty to give Barça a 3-2 win at the Mestalla, and several players were struck by missiles thrown from the crowd as the visitors celebrated.
Luis Suarez and Neymar both went down, and team-mates had to restrain a furious Messi who shouted at and celebrated wildly in front of the home supporters.
Earlier Barcelona substitute Paco Alcacer, a former Valencia player, was hit with a bag of sunflower seeds.
Barcelona coach Luis Enrique refused to comment directly on the incident at the end of the game, saying only:
"We've celebrated a goal as you have to celebrate a winning goal against a rival that's made things so difficult."
Valencia coach Cesare Prandelli said he did not see the incident.