The 2-0 win at tiny Eibar, a side playing in La Liga for the first time and which has now lost eight games in a row, may not seem like an unexpected achievement.
But, with a European Champions League last-16 decider at home to Manchester City on Wednesday and then the "El Clasico" crunch clash with bitter rival Real Madrid next Sunday, every win is vital at this stage of the campaign.
"We're going into the Clasico as leaders and in perfect form," Barca coach Luis Enrique said. "But first we have to focus on City because qualification is at stake. Then we'll see what happens at the weekend."
Messi has now scored 43 goals this season, first netting a 31st-minute penalty after Borja Ekiza unluckily handled the Argentine's blocked shot and then bulleting in a header from Ivan Rakitic's corner 10 minutes after the restart.
"Eibar didn't look like a team that has just lost seven in a row," said Enrique, who welcomed back Brazil star Neymar from suspension to resume his role up front with Messi and Luis Suarez.
"They played good football and they fully deserved their great start to the season. I don't think they'll have any trouble avoiding relegation."
The result puts even more pressure on second-placed Real Madrid to win Sunday's home clash with Levante.
The European champion's coach Carlo Ancelotti has been criticized after a poor run of results since the turn of the year, while world-record signing Gareth Bale has particularly been vilified by national sports paper Marca
following Tuesday's home defeat by Schalke.
Real can take some small consolation in the fact that city rival Atletico Madrid could only draw 0-0 at Espanyol, meaning the defending champion stayed fourth in the table following Valencia's 2-0 win over Deportivo La Coruna on Friday.
Atletico defender Miranda was sent off in time added on at the end of the first half for a foul on Abraham.
Diego Simeone's side hosts German club Bayer Leverkusen on Tuesday as it seeks to overturn a 1-0 deficit and seek to match last season's achievement of reaching the Champions League final.
Barca, also looking to join Real in the quarterfinals, faces a City side reeling after Saturday's 1-0 defeat by relegation-threatened Burnley.
It left Manuel Pellegrini's team five points behind English Premier League leader Chelsea, which has two games in hand ahead of Sunday's home clash with Southampton.
"We must continue to fight but the chances of winning the title are far as things stand," said Pellegrini, whose team must overcome a 2-1 deficit at the Nou Camp next week.
"There is still a chance, but it is more difficult after this result. We needed to create more chances than we did and find more space in and around their defense."
The Chilean refused to blame the referee for not awarding what appeared to be a clear penalty for City in the dying minutes, when Pablo Zabaleta was brought down in the box.
"Was it a penalty? Maybe, but the referee decides these moments and I don't think that was the most important thing in this game," he said.
"The issue for us at present is that we are not winning the games that we normally do, especially against teams we are expected to beat, and that is because we are not scoring goals."
City, seeking to retain its EPL title, is only one point ahead of third-placed Arsenal after Arsene Wenger's team won 3-0 at home to West Ham on Saturday.
The London side has now won four games in all competitions since suffering a shock 3-1 home defeat by Wenger's former club Monaco
in the first leg of their last-16 Champions League tie last month.
"We have to believe that we can do it," the Frenchman said of Tuesday's trip to the principality. "This time Monaco are favorites so we have to go there, give absolutely everything and come out of the game with that feeling."
Monaco moved up to fourth in the French league on Friday, beating nine-man Bastia 3-0 as Anthony Martial scored twice and Lavyin Kurzawa missed a penalty.
Italian club Juventus, another side in Champions League action next week, went 14 points clear in Serie A with a 1-0 win at mid-table Palermo on Saturday.
Spanish substitute Alvaro Morata ended Palermo's six-month unbeaten home run with a curling winner to maintain the Turin team's momentum ahead of Wednesday's trip to Borussia Dortmund.
The German side, which trails 2-1 after the first leg thanks to goals from Morata and Carlos Tevez, drew 0-0 at home to Cologne Saturday to remain in mid-table after a second successive scoreless draw in the Bundesliga.
Defending champion Bayern Munich moved 14 points clear at the top with a 4-0 win at Werder Bremen, as Poland striker Robert Lewandowski scored twice to add to his goal from the midweek Champions League thrashing of Shakhtar Donetsk.
Thomas Muller, who netted twice in the 7-0 routing of the Ukrainian side, opened the scoring while David Alaba bagged the second goal.
Third-placed Leverkusen, meanwhile, triumphed 4-0 over Stuttgart on Friday, with Josip Drmic scoring two.
Wolfsburg, eight points ahead of Leverkusen, hosts second-bottom Freiburg on Sunday.