Messi was celebrating Barca's 94th-minute winner with his team mates near the corner flag at the Mestalla stadium on Sunday when someone threw the bottle from the stands.
To add insult to injury the Argentina captain was then booked for time wasting.
Messi was examined by a member of Barca's medical staff after the final whistle and did not appear to be hurt, giving the thumbs-up as he walked off the pitch.
"Valencia regret and condemn the isolated incident in the game against Barcelona in which a small, uncapped bottle of water was thrown from the stands at opposition player Lionel Messi," the club said on their website (www.valenciacf.com).
"The club will endeavour to locate the person who threw the bottle and they will be banned for life from the Mestalla. Valencia operate a zero tolerance policy on such actions and rigorously enforce all security measures set out by legislation."
Barca's 1-0 win kept them hard on the heels of leaders Real Madrid who are two points clear of their arch-rivals after 13 matches thanks to Saturday's 2-1 victory at Malaga.
The Catalan club said on Monday they would appeal against the yellow card given to Messi.
The referee said in his match report that it was shown because the player "delayed his return to his half of the pitch after the goal was scored with the intention of wasting time".
(Reporting by Iain Rogers, editing by Ed Osmond and Tony Jimenez)
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