The fans threw rocks at the luxury cars early Thursday, shortly after the team lost to 2-0 to Deportes Tolima in Colombia.
Other fans demonstrated at the airport, but the team left through a back exit with a police escort. Protest messages were painted on the walls of the team's headquarters, some against star striker Ronaldo.
Corinthians has been under pressure from its fans since last year, when it failed to win any titles while celebrating its centenary. The Copa Libertadores is the only major championship the team is yet to win.