The Catalan club released an angry statement expressing their "surprise and outrage" at the punishment dished out to their star player describing him as an "exemplary sportsman".
The Argentina forward was also fined 10,000 Swiss Francs (£8,100) by FIFA on Tuesday for "having directed insulting words" at an official during his side's World Cup qualifier with Chile last Thursday.
He was caught on camera venting his fury at an assistant who signalled he had committed a foul late on in Argentina's 1-0 win. He was not shown a card at the time.
The 29-year-old missed Tuesday's 2-0 loss to Bolivia and will also be banned for Argentina's next three World Cup qualifiers, unless an appeal is successful.
Messi will miss the qualifiers in Uruguay in August, at home to Venezuela the following month and at home to Peru in October, meaning he will only be able to return for Argentina's final qualifying match away to Ecuador.
His international absence should benefit his club side, but Barca have still issued a strong statement condemning the sanction.
The club said: "FC Barcelona express their surprise and outrage at the official decision of the FIFA disciplinary committee to sanction Leo Messi after the World Cup qualifying match between Argentina and Chile.
"The club consider the four-game ban imposed upon the player unjust and totally disproportionate.
"Finally, FC Barcelona want to reiterate their support for Leo Messi, an exemplary sportsman for his behaviour on and off the pitch."
Argentina's defeat to Bolivia left them with a fight on their hands to qualify for the World Cup in Russia.
They lie in fifth place in the South American qualifying group, with only the top four guaranteed qualification, although only two points separate them from second-placed Colombia.
Messi's continued absence could, therefore, prove costly, although Argentina have promised to appeal, with Jorge Miadosqui, the Argentina team secretary, saying: "The decision doesn't correspond with the reality based on what was put in the referee's report."
FIFA said when announcing its decision that the suspension was "in line with the FIFA disciplinary committee's previous rulings in similar cases".