The little magician appeared to pick up a problem to right his arm or shoulder, and was replaced by Ousmane Dembele.
In the 17th minute of the La Liga clash, Messi crumpled to the ground after tussling with Franco Vazquez.
He received treatment on the pitch and then on the touchline, before returning to action.
But he only managed another five minutes before he was forced off.
The Barca star had put his side into a 2-0 lead with just 12 minutes on the clock, after assisting Philippe Coutinho for the opener just two minutes in.
Messi could now be a huge doubt for Barcelona's Champions League clash against Inter Milan on Wednesday night.
Then there is the small matter of El Clasico.
Ernesto Valverde's side will welcome Real Madrid to the Nou Camp in a week's time.
And the Catalans will have been confident of getting bragging rights over their great rivals, as Los Blancos' tough start continued with a 2-1 defeat to Levante this weekend.
But without their star man, Barca may have to rethink that game-plan.
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