The strike makes Messi the second player to have scored 400 goals in any of Europe's top five leagues, reaching the milestone in 63 games fewer than Cristiano Ronaldo did, and he has now almost doubled Alan Shearer's Premier League record of 260 strikes.
Ronaldo is the second-highest goalscorer in LaLiga history with 311 goals, and has 412 goals across Portugal's Liga NOS, the Premier League, LaLiga and Serie A.
"He is from another galaxy", his coach Ernesto Valverde said.
"They are incredible. Not only the goals, but also what he creates".
The former Liverpool FC number 10 opted to move to FC Barcelona to link up with his ex-Reds strike partner Luis Suarez and Argentina legend Lionel Messi. It was Coutinho and Suarez and the Argentinian who linked up and Messi applied the low finish into the bottom corner.
But Messi's score against Eibar got him to 400 goals 63 games earlier than Cristiano Ronaldo.
Messi's moment came in the 53rd minute and it was Suarez who started it, stealing back possession after a heavy touch from Anaitz Arbilla.
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Barca were not at their best but were too strong for Eibar and their victory maintained a five-point lead at the top of the table.
He alone supplied three passes in the build-up to Suarez's opener.
"He was the one who left", Cardoner said in October. No team has scored more in La Liga.
Third-placed Sevilla lost 2-0 at Athletic Bilbao, ending its unbeaten run in nine rounds.
However, he has found life more hard in his second season and has started only one of Barca's last five fixtures: the 1-1 draw at home to Tottenham in December when coach Ernesto Valverde picked a weakened XI with first place in the group already secured.
Bilbao forward Inaki Williams scored both goals for the hosts to help lift them out of the relegation zone.