The Spanish champions, Real Madrid won 3-1 away from home in the first El Clasico of the season.
After just five minutes, Karim Benzema fed a through pass to Fede Velverde who in return, opened the scoring.
Madrid’s lead lasted, however, for just three minutes as Barcelona replied when Messi found Jordi Alba who in return found Fati for the equalizer.
In the 67th minute, Sergio Ramos scored from a controversial penalty call before Luka Modric in the 90th minute took the game beyond the Catalans.
Meanwhile, under new coach Ronald Koeman, Barca are now without a three-in-league win and are placed six points back in the mid-table.
While their closest rival, Madrid moved to first in the table with 13 amassed points so far.