Ernesto Valverdes side are playing the penultimate game of their La Liga season and have already been crowned champions.
But Messi will play no part in the match and stayed behind in Barcelona while his teammates travelled to Levante.
Messi is understood to be rested for the game as he is expected to feature in Barcas friendly against Mamelodi Sundowns in South Africa on Wednesday.
Barcelona will then return to Spain to play their final La Liga match of the season against Real Sociedad on Sunday.
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