The 30-year-old came into the game at Camp Nou on 599 for club and country and reached the latest landmark of a phenomenal career in the 26th minute.
After being brought down by Thomas Partey 25 yards out, Messi curled a sumptuous trademark free-kick over the wall and into the top-right corner, Jan Oblak unable to keep it out despite getting a hand to the effort.
Messi's 600 was brought up a day after great rival Cristiano Ronaldo reached 300 LaLiga goals, the Real Madrid superstar netting a brace in Sunday's 3-1 home win over Getafe.
Below, the numbers behind Messi's latest milestone have been crunched, thanks to Opta.
99 - Messi has scored his goals against 99 different opponents. Atletico Madrid (28) is second on his list of favourite teams to face, one behind Sevilla.
373 - The Argentine's strike against Atletico was his 373rd in the Spanish top flight. Ronaldo — on 301 after his double on Sunday (AEDT) — is the only other man to pass 300.
38 - Messi has netted a hat-trick on 38 occasions for club and country. On five occasions he has scored four goals, and his best effort for a single game remains the five he scored against Bayer Leverkusen in the UEFA Champions League in 2012.
82 - His most prolific season was the 2011-2012 campaign, where he scored an extraordinary 82 times. Part of that tally contributed to 91 in 2012 — a career-best for a calendar year.
1 - Although Messi has produced almost a quarter of his goals (148) between minutes 76 and 90, he has only once netted in extra-time. That was the winner in the 2009 FIFA Club World Cup final against Estudiantes.
496 - The amount of goals Messi has scored with that magical left foot. He has 78 with his right, 24 with his head and two with other parts of his body.
96 - Nearly one in six of Messi's goals have come from outside the box, proving he is a threat from almost anywhere on the field.
77 - Although more fallible from the spot than someone of his quality ought to be, Messi still has 77 successful penalties to his name. He has also netted from 39 free-kicks.
42 - The most frequent provider of Messi's goals has been Dani Alves, now plying his trade at Paris Saint-Germain. Of Messi's current team-mates, Andres Iniesta (36) has supplied him with the most assists.