Barca's initial appeal was rejected by the RFEF's competition committee and the club lodged a second challenge with a higher appeals committee which ruled in their favour on Thursday.
The RFEF said on its website (www.rfef.es) the committee had been unable to detect "deliberate time-wasting" on Messi's part but only "a normal reaction from someone who had suffered an aggression by a spectator".
Messi was celebrating his side's 94th-minute winner with his team mates near the corner flag at the Mestalla stadium when a plastic bottle was thrown from the stands and appeared to strike him on the head.
He was examined by 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 about the incident.
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.
Real can extend their club-record winning streak in all competitions to 18 games when they host Celta Vigo on Saturday before Barca welcome city rivals Espanyol on Sunday.
(Reporting by Iain Rogers, editing by Ed Osmond)
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