The Argentine, who has been the competition's all-time top scorer since 2014, struck the second goal of a 3-0 win at the Nou Camp early in the second half, rounding a defender and slotting into the bottom corner with his left foot.
Messi, who is also the club's all-time top scorer and has won nine league titles and four Champions League titles there, was given a fittingly ecstatic reception by the Barca fans.
"Obviously, we have to be very proud of Messi because every week he demonstrates how good he is and continues to make history with the club," said Luis Suarez, who scored Barca's other two goals in a win that kept them five points clear at the top of La Liga.
Messi, named Barca captain at the start of this season, was making his 435th La Liga appearance for the club where he has spent his entire career, having made his league debut in 2004.
"His numbers are stratospheric, they are incredible," said Barca coach Ernesto Valverde.
"But it's not just goals, it's everything else he does too."
(Reporting by Richard Martin, editing by Ed Osmond and Ian Chadband)
