The 29-year-old Barca forward was suspended for directing "insulting words" at an assistant referee during Thursday's 1-0 win over Chile.
He remains free to play for his Spanish La Liga club.
"The club considers the four-match suspension finally imposed on the Argentine player to be unfair and totally disproportionate," the club said.
"Finally, FC Barcelona wishes to reiterate its support for Leo Messi, an exemplary player in terms of conduct both on and off the pitch."
Messi is set to be banned for three of his country's four remaining qualifiers.