Manager Gerardo Martino said on Tuesday that whether his star player was available or not would come down to a game-time decision, and when the lineup was revealed ahead of the final at DRV PNK Stadium, Messi was not listed on the team sheet.
Messi's former Barcelona teammate Jordi Alba is also unavailable as he deals with an injury of his own.
Messi has been in and out of Miami's lineup since returning from international duty for Argentina with a leg injury related to an old scar tissue problem. He did not play in a loss to Atlanta United on Sept. 16, then tried to play on Sept. 20 against Toronto FC, but was withdrawn after about 30 minutes in a game Miami went on to win 4-0.
Alba was substituted with muscle fatigue in the Toronto game shortly before Messi, and after the match Martino said neither would play in last Saturday's game away to Orlando City. Miami managed a draw in that match to keep its MLS Cup playoff hopes alive.
Messi's impact on Miami since arriving in July in a blockbuster deal has been remarkable. He's scored 11 goals and contributed to a total of 16, with the team having never lost a game in which he played.
Miami is five points behind New York City FC, which it faces on Saturday in MLS, in the standings for the final playoff spot with five games to play and two games in hand.