Barcelona captain has now scored more goals for a single club than any other footballer.
Messi achieved the feat in the 65th minute, helped by 18-year-old Pedro “Pedri” Gonzalez.
After receiving the ball near the edge of the area, Pedri deftly rolled his boot over the ball to push it behind him to meet the Argentine’s run.
The slick pass left Messi clear to beat goalkeeper Jordi Masip, who had denied him twice.
“When I started playing football I never thought I’d break any record, especially not the one I achieved today that Pele held,” Messi wrote on Instagram after the match.
“I can only give my thanks to everyone who helped me during these years, my teammates, my family, my friends, and everyone who supports me every day.”
It is yet another record for Messi, who joined Barcelona at age 13 and made his competitive debut at 17 in 2004.
“[The win] shows that we have a strong squad, where there is a lot of competition for playing time,” Barcelona coach Ronald Koeman said.
“It proves that, with a calendar packed with games, we can rest some players. We got this win by playing good football. The team was focused from the start.”
Barcelona stayed in fifth place at eight points behind Atletico Madrid.
Pele congratulates Messi
On Saturday, after Messi scored his 643rd goal and equalled Pele’s record, the Brazilian great praised him on Instagram.
“When your heart overflows with love, it is difficult to change your path,” he wrote.
“Like you, I know what it’s like to love wearing the same shirt every day. Like you, I know that there is nothing better than the place we feel at home.
“Congratulations on your historic record, Lionel. But above all, congratulations on your beautiful career at Barcelona. Stories like ours, of loving the same club for so long, unfortunately will be increasingly rare in football. I admire you very much, Leo Messi.”
Pele, 80, made his debut at Santos in 1956 at the age of 15 and played for the club until 1974, featuring in a total of 665 competitive games.
Messi, 33, tried to force his way out of Barcelona in the summer but was frustrated as then-president Josep Maria Bartomeu refused to let him walk away for free.
The captain has since reiterated his commitment to the club, with whom he has a contract until the end of the current season, although there remains a lot of speculation about his future.
Messi also holds the record for most Ballon d’Or wins, claiming his sixth in 2019.
