Thigh injury ends Messis season - club
The Argentine striker has a right thigh strain that will prevent him from playing for between two and three weeks and will not feature again this season, as La Liga ends on June 1.
Barcelona secured the league title -- their fourth in five seasons -- on Saturday when second-placed Real Madrid were held to a 1-1 draw at Espanyol.
The following day Messi started against Atletico at the Vicente Calderon but was forced to come off in the 72nd minute, leaving Barca with 10 men as all three substitutes had already been used.
The end of Messi's season has been plagued by injuries, with a hamstring injury suffered while playing against Paris Saint-Germain in the quarter-finals of the Champions League last month limiting his involvement in recent weeks.
The 25-year-old has scored 46 goals in La Liga this season.
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