Messi, who had recovered from a calf injury to feature, was replaced at the start of the second half after suffering a thigh problem.
The Argentine, making his 400th La Liga start, provided the corner for Antoine Griezmann to head home off the bar before Arthur made it 2-0.
After the game, Barca boss Ernesto Valverde described Messi's injury as a "small problem in the adductor".
"When something happens to Messi, everyone stops, not only on the field, but in the stands as well," he said.
"As a precaution we have decided not to risk it. In theory, it is nothing more but we will see tomorrow how it is."
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