With 26 minutes on the clock, Barca were awarded a free kick outside their visitors' box, and Messi executed a shot that had too much pace on it for Jan Oblak to keep out. The shot-stopper got a touch to the effort but could not claw it away.
It was Messi's third goal from a direct free kick in as many matches and brought up fresh milestone for the Argentine attacker.
In his 747th appearance for Barcelona, he has now netted 539 times, while for Argentina he has found the target on a more modest 61 occasions in 123 outings.
The 30-year-old debuted for Barca in the 2004-05 season and has since amassed incredible figure, having scored at least 40 goals in all competitions for his club side in each season since 2009-10.
Although he has not reached that tally yet, his strike against Atleti was his 32nd of the season, attained in 41 appearances.
It was also his 24th of the season in La Liga, thereby carrying himself further clear of the chasing pack in the race to finish as the division's top marksman. Team-mate Luis Suarez is second with 20 goals, while great rival Cristiano Ronaldo is joint third, on 16 for the season, level with Celta attacker Iago Aspas.
Messi's strike was also Barcelona's 100th of the campaign in all competitions.