Barca's initial appeal was rejected by the Spanish football federation's (RFEF) competition committee on Wednesday and the club responded by saying they would lodge a second challenge with a higher committee.
Messi was celebrating Barca's 94th-minute winner with his team mates near the corner flag at the Mestalla stadium when the bottle was thrown from the stands.
He was examined by a member of Barcelona's medical staff after the final whistle and did not appear to be injured, giving the thumbs-up as he walked off the pitch.
It was not clear if the bottle or another object, such as a coin, had struck the Argentina captain and he has made no public comment on the incident.
"In response to the verdict (on Wednesday), FC Barcelona has decided to go to the Appeals Committee and request the booking be withdrawn," Barca said on their website.
The referee said in his match report he showed the card because Messi "delayed his return to his half of the pitch after the goal was scored with the intention of wasting time".
Valencia vowed to ban the bottle-throwing fan from the Mestalla for life once the person had been identified.
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.
Messi and a host of other regulars including Neymar and Luis Suarez have been rested for Barca's King's Cup last-32, first leg at third-tier Huesca later on Wednesday.
(Reporting by Iain Rogers, editing by Ken Ferris and Toby Davis)
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