The Argentine created the opener for Xavi and then got on the scoresheet himself after Neymar had volleyed the Blaugrana's second
The Argentina international went into the match needing just two goals to go level on 251 top-flight strikes with Athletic Bilbao legend Telmo Zarra, but he could only notch once as he was frustrated by Eibar goalkeeper Xabi Irureta.
Messi saw a couple of chances go begging in the first half, as he was first denied by the right leg of Irureta, before flashing an effort just wide.
In fact, Eibar should have taken the lead themselves before the break, as Ander Capa and Saul Berjon both failed when through on goal.
Xavi eventually gave Barca the lead with an hour gone following a clever pass from Messi and Neymar netted the second 18 minutes from the end to effectively secure the victory.
Messi rounded off a delightful move in the 74th minute to ensure Barca stay four points clear of Real Madrid, with the Argentinian now eyeing a record-breaking day against their bitter rivals at the Santiago Bernabeu in a week's time.
Luis Enrique was keen to divert his players' attentions away from records in the build-up, demanding focus on the match itself instead.
But unsurprisingly all eyes were on Messi and he took centre stage, seeing numerous opportunities slip from his grasp before the best chance to break the deadlock arrived in the 20th minute.
The Argentine played an incisive one-two with Dani Alves down the right flank, before seeing his effort well blocked by Irureta from point-blank range.
Messi's determination was obvious and he went close again five minutes later, sending a fierce drive just wide of the top-right corner from 20 yards.
The hosts continued to monopolise possession as the first half progressed, but the visitors spurned good sights of goal just before the break.
Capa coolly took the ball past Claudio Bravo before shooting into the side of an empty net, while the Chilean was forced into making a save as he denied Berjon when one-on-one.
The hosts seemed to struggle during the early stages of the second period, but they did eventually break the deadlock.
Although Messi may not have got the goal himself, the 27-year-old played a pivotal role as he fed a fine throughball into the area for Xavi, who lifted a clever finish over Irureta.
Barca ensured the final stages would not be remotely tense as Neymar volleyed in a Dani Alves cross 18 minutes from time, before Messi played a fantastic one-two with the Brazilian forward and fired into the bottom-right corner.
Though Messi went close to equalling the record late on, the 250th goal of his Liga career sets him up nicely as he looks to equal - if not surpass - Zarra's fabled milestone on the grandest of stages next week.