After an unusually quiet first 45 minutes, Messi burst into life after the restart and claimed his milestone goal – his 13th in eight appearances against Eibar.
Luis Suarez had given Barca the lead with their only shot on target in the first half, and he doubled his tally six minutes after Messi's moment in the spotlight with a composed finish from a tight angle.
Messi took up more of a playmaker role in the opening exchanges and created half-chances that Gerard Pique and Jordi Alba were unable to convert.
Suarez showed them how it should be done in the 19th minute after a slick interchange with Philippe Coutinho opened up the Eibar defence, the Uruguayinternational finding the bottom corner with unerring accuracy.
Despite falling behind, Eibar continued to push forward and Sergi Enrich should have done better from Ruben Pena's cross, however the striker headed wide of Marc Andre ter Stegen's goal.
Coutinho felt he should have had a penalty minutes before the break but his claims were waved away despite Pena's clumsy tackle inside the area.
After the lacklustre opening salvo, Barca had much more urgency to their game after the break and eight minutes into the second period Messi got his landmark goal.
Having received the ball from Suarez, the five-time Ballon D'Or winner made himself some space before firing low under Asier Riesgo.
Suarez then notched his 14th league goal of the campaign to extend Barcelona's advantage, before Ter Stegen needed to be alert to keep out Pablo De Blasis' close-range header.
Ernesto Valverde introduced reported Manchester City target Ousmane Dembele with 18 minutes to play, but despite looking lively he was unable to stretch Barca's lead on what ultimately turned out to be a comfortable victory despite the league leaders being far from their fluent best.
Lead restored for Barca
After seeing their advantage cut to two points by Atletico Madrid earlier on Sunday, Barca restored their five-point cushion with ease on Messi's historic night. For Eibar the defeat means they have failed to win their last six LaLiga clashes, and sit just three points above the relegation zone.
Suarez the scourge of Eibar once again
While Messi will grab the headlines, Suarez deserves a lot of credit after a sublime double to continue his fine scoring run against Eibar. The Uruguay international has now scored in his last six matches against Sunday's opponents, his two goals both superbly taken.
