Barca have once again proved to be the best that Spain have to offer, with a total of 87 points seeing them finish the season 11 points clear of their nearest challengers Atletico Madrid.
The Catalan giants fell short in the Champions League this season, but they will have the chance to complete another domestic double when they face Valencia in the Copa del Rey final next weekend.
Barca were missing a number of first-team players for the clash in the Basque Country, with Arthur, Philippe Coutinho, Ousmane Dembele, Luis Suarez and Marc-Andre ter Stegen amongst those unavailable.
Barca had a decent chance to make the breakthrough in the fourth minute when Roberto broke into the Eibar box before feeding Messi, but the Argentine was crowded out at the vital moment.
An extremely entertaining first 10 minutes continued to produce opportunities, with Sergio Busquets striking wide of the post from distance after Marko Dmitrovic had left his goal, before Fabian Orellana had a dangerous low cross turned wide of Cillessen's post down the other end of the field.
Charles then tested Cillessen shortly after as Barca continued to come under pressure from the impressive hosts, who were seemingly desperate to give their fans something to cheer in the final match of the 2018-19 La Liga season.
Barca were level in the 31st minute, however, when Messi collected a super pass from Arturo Vidal before sliding the ball under the onrushing goalkeeper.
Less than one minute later, Messi had his second. Vidal picked out the Argentine with a brilliant ball for his first, but this time the pass came from Ivan Rakitic as the Croatian split the Eibar defence.
There was a hint of offside about the run, but Messi was in his own half and the attacker drove into the Eibar box before lifting the ball over Dmitrovic to make it 36 league goals for the campaign.
Eibar levelled the scores in the final stages of the first half, however, when Pablo De Blasis showed wonderful technique to loop a half-volley over Cillessen from distance.
The home side also had the first real chance of the second period when Enrich met a smart cross from De Blasis, but Cillessen was on hand to make an excellent low save.
The Barca goalkeeper then had to keep out a header from Charles before Orellana missed the post minutes later as the visitors came under huge pressure in the first 10 minutes of the second half.
Pique had a chance to score a third for the champions just past the hour after breaking forward from the back, but Dmitrovic was on hand to make a smart save, before the Spanish centre-back failed to meet a low Malcom cross in the next attack.
Carles Alena replaced Busquets in the 65th minute as Valverde turned his attentions to the Copa del Rey final against Valencia next weekend.
Eibar continued to come at the away side, though, and Orellana sent one wide of Cillessen's post before Kike replaced Enrich as Mendilibar looked for something different in the final third of the field.
Carles Perez was the third player off the Barca bench as the 21-year-old was handed his first-team debut, replacing the ineffective Malcom down the left.
It was another poor performance from the Brazilian and it would not be a surprise to see the attacker sold this summer, particularly with Antoine Griezmann expected to arrive from Atletico Madrid.
Eibar, who have finished the season in 12th, had a big chance to score a third in the 82nd minute when Cucurella found space inside the Barca box, but the on-loan defender somehow fired over the crossbar.
The point means that the champions have not only finished the season 11 points clear of second-placed Atletico, but 19 clear of third-placed Real Madrid, who lost at home to Real Betis earlier in the afternoon.
EIBAR (4-4-2): Dmitrovic; Cote, Ramis (Alvarez 77'), Oliveira, De Blasis; Cucurella, Jordan, Escalante, Orellana; Charles (Cardona 85'), Enrich (Kike 66')
BARCELONA (4-3-3): Cillessen; Semedo (Wague 46'), Pique, Lenglet, Alba; Vidal, Busquets (Alena 65'), Rakitic; Roberto, Messi, Malcom (Perez 73')