That took Messi to 500 in 592 games for the Catalan club, including friendlies, with 469 of those in official fixtures.
Messi is now 105 goals clear of second all-time top scorer Paulino Alcantara, who played for Barcelona in two spells between 1912 and 1927.
In April, the forward scored his 500th career goal, including internationals, in Barcelona’s 2-1 defeat by Valencia.
Messi’s first senior goal for the La Liga club came as a 17-year-old against Albacete in May 2005.
The Argentine has now scored 320 goals in Spain’s top flight, to add to his 90 in the Champions League.
The rest of Messi’s official Barcelona goals have come in Spanish cup competitions, the Uefa Super Cup and Fifa Club World Cup.
He broke Barcelona’s goals scored in official matches record – previously held by Cesar Rodriguez, who played for the club in the 1940s and 1950s – in 2012.