Atletico arrived at the Camp Nou on the back of eight consecutive wins but Barca halted the surge and instead restored their own lead at the top to eight points, with 11 games left to play.
Messi proved the difference again, his bending first-half strike worthy of winning any contest and taking his own career tally to an astonishing 600 goals, 539 for Barca and 61 for Argentina.
The only blot on a dominant Barcelona performance was an injury to Andres Iniesta, who had to be substituted after 34 minutes with what the club confirmed was a strain in the back of his thigh.
Iniesta now has 10 days to recover before next week’s Champions League second leg against Chelsea.
The build-up to this contest, labelled ‘the Grand Final’ by sections of the Spanish press, was driven by talk of a Barcelona dip following three draws in five league games, with the in-form Atletico primed to move within two points of their rivals.
But Diego Simeone’s strategy of absorb and counter failed to pay off here and, in the end, the visitors might easily have been beaten by a more emphatic scoreline.
Atletico striker Antoine Griezmann, meanwhile, who came in with seven goals in two games, was largely anonymous.
Ernesto Valverde made a statement of attacking intent by plumping for the more creative Philippe Countinho over Paulinho but his team took a while to find their rhythm.
Even Messi hit the wall with a poor free-kick and then sent a cross-field switch straight into the advertising boards.
The Argentinian shook his head but soon recovered, moments later escaping a cage of four Atletico defenders before driving a shot straight at Jan Oblak.
For all Atletico’s discipline and defensive rigour, one mistake in the 26th minute was all it needed. Thomas Partey clipped the back of Messi’s foot 25 yards out and the forward whipped the free-kick beyond the scrambling Oblak and into the top corner.
The rest of the half was a picture of Barca dominance, interrupted only by the injured Iniesta being replaced by Andre Gomes and a handful of minor skirmishes, the most noteworthy of which saw Messi hack down Filipe Luis and earn a yellow card.
Atletico’s demise was summed up by Luis tripping over his own feet during a rare attack down the left but half-time helped the visitors, who were more competitive after the break.
Luis Suarez thought he had scored a second after half-volleying through Oblak’s legs but was flagged offside, before Jose Gimenez applied a crucial block to deflect a Messi shot over.
There was one nervy moment for the hosts five minutes from time as Diego Costa headed down for Kevin Gameiro to slam home. Costa, however, had strayed offside and Barca held on for what will surely prove a crucial three points.
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