It was a first start of the season for Messi, who had recovered from a calf strain, but he did not make it beyond half-time and was replaced by Ousmane Dembele.
Barcelona boss Ernesto Valverde said Messi picking up any has an impact on more than just his team-mates.
“It’s some discomfort in the abductor and so we didn’t want to risk it,” he said.
“When something happens to Messi, the world stops.