Messi was marked as absent on the team sheet and Barcelona, who were facing Asian champions Guangzhou Evergrande, said in a statement that the Argentine was suffering from "renal colic".
"His availability for the next matches will depend on his progress," the statement added.
Barcelona were also without injured forward Neymar for the game. The winners meet South American champions River Plate in Sunday's final.
(Reporting by Brian Homewood; Editing by John O'Brien)
