The Barcelona star picked up a muscular injury this weekend and is one of a number of withdrawals from Wednesday's friendly with Germany.
The forward, who starred for the Albiceleste this summer in Brazil, featured throughout Barcelona's 1-0 win at Villarreal on Sunday but the club confirmed afterward that he had picked up a knock at El Madrigal.
Barca's report to the AFA said: "The player suffered a muscle strain in his right hamstring and needs rest as a precaution."
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Messi, who has been replaced by Tottenham's Erik Lamela, is not the only late withdrawal from Gerardo Martino's first match as Argentina boss for the clash with newly crowned world champion Germany on Wednesday in Dusseldorf.
Albiceleste veteran Maxi Rodriguez suffered tightness in his hamstring, Inter striker Rodrigo Palacio's left ankle is bruised and Zenit defender Ezequiel Garay's left leg has been causing him muscular pain ahead of the international break, and all three players will miss out on the match.
Paris Saint-Germain attacker Ezequiel Lavezzi is still to be evaluated by Argentina's medical team after complaining of a backache following his club's 5-0 victory over Saint-Etienne on Sunday.