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The Argentine superstar missed out on this evening's game due to an ankle injury but was still inside the Camp Nou to watch.
Barcelona failed to win all three points and it means they go into 2021 sixth in La Liga, six points behind leaders Atletico Madrid.
Cameras caught Messi's immediate reaction as the whistle blew and he shook his head before walking off.
Messi's frustrated figure comes days after he conducted an interview with Argentine outlet La Sexta outlining his Blaugrana future.
He nearly left Barcelona last summer in an incredibly public transfer saga, but chose to remain with the club.
"These days I am feeling well," Messi said. "I had a really bad time last summer with the burofax and all that, and before.
"But now I feel good, excited to fight for everything in front of us. But the club are going through difficult moment, the team too. Everything around Barca is difficult.
"I know that things at Barca are really, really bad. It will be difficult to get back to where we were."
Eibar took the lead in the second half, following a mistake from young defender Ronald Araujo.
Araujo attempted to play out from the back and got caught on the ball by Kike, who ran through unopposed to slot past Marc-Andre Ter Stegen.
Barcelona managed to get back in the game through substitute Ousmane Dembele but couldn't find a winner.
A defensive error leads to Eibar taking the lead! :scream:- Premier Sports :tv: (@PremierSportsTV) December 29, 2020
Kike Garcia piles on the misery for Barca :eyes: pic.twitter.com/pT3Thu2pIZ
Araujo took ownership for his mistake at the end of the game and spoke to Spanish media, apologising for his mistake.
He begun per barcacentre: "The mistake? I take full responsibility. It's a problem of concentration. It's a shame, but now we have to look up and move on.
"Our style is to take risks, but you can't lose balls like the one I lost."
Do you think Lionel Messi will leave Barcelona this summer?