The Argentina international was hit by the object during Barca's celebrations after Sergio Busquet's dramatic injury-time goal secured a 1-0 win at Mestalla.
Referee Fernandez Borbalan booked the forward, stating in his match report that Messi had: "Delayed his return to the pitch after the goal was scored, in order to waste time".
The incident drew a quick response from Valencia, who vowed to identify the supporter and issue them with a lifetime ban.
Though the booking would not have caused Messi to miss any game time, it has nevertheless been withdrawn by the RFEF (Spanish Football Federation).
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