The World Player of the Year called for the change after tumbling in a challenge and was replaced by Andres Iniesta in the 21st minute.
Messi has damaged the hamstring in his left leg and will undergo further tests on Monday, the champions said in a statement on their official Twitter feed.
The Argentina international has suffered a string of muscle problems at the start of this campaign and has struggled to reach his best form to date.
(Reporting by Mark Elkington, editing by Alison Wildey)
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