The reigning champions wasted little time claiming the lead as a 14th-minute Messi strike left them a goal to the good before a quickfire double from the captain widened that margin going into the break.
A rallying Eibar failed to profit from a handful of second-half chances before their fate was irreparably sealed by a fourth Messi goal and a last-minute strike from Arthur, with recent emergency signing Martin Braithwaite also making his debut from the bench and a late impact on the game.
The victory sees the club push to the head of the table, with long-time rivals Real Madrid demoted to second ahead of their visit to Levante on Saturday night.