The Argentina captain converted after 50 minutes to put his team 2-1 ahead against Diego Simeone’s side.
Atletico’s two goals were through penalties scored by Saul Niguez while Barca first scored through a Diego Costa own goal while Messi scored in the second half.
Barca are now one point behind Real Madrid in second having played one game more than their rivals. Atletico Madrid are two points clear of Sevilla and remain in third place, 11 points behind Barca.
Messi has now scored 630 for the Catalans, making him the club’s all-time top scorer by some distance, with another 70 strikes coming in international colours for Argentina.
Messi alongside Ronaldo (who has 725 career goals) joins a select few of football legends such as Josef Bican , Romario, Pele, Ferenc Puskas, and Gerd Muller who have scored over 700 goals in their careers.