Barcelona believes the four-game ban FIFA imposed on Messi for abusing an assistant referee is unjust and disproportionate.
The La Liga giants expressed their outrage in a statement, saying Messi is of exemplary conduct.
The Argentine was caught on camera venting his frustration at a linesman who signalled he committed a foul late on. His action was caught on camera.
Messi missed the 2-0 loss to Bolivia and will miss their next three matches against Uruguay, Venezuela and Peru. Unless an appeal is won.
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.”