Barca were ahead after just two minutes as Philippe Coutinho collected a pass from Messi before burying the ball into the top corner.
Any joy at jumping above in-form Sevilla, however, was tarnished by Messi´s injury, which will now rule him out of next weekend´s Clasico against Real Madrid. The approximate time off is three weeks.
"It's a significant loss, given who we're talking about", Barcelona manager Ernesto Valverde said in a postmatch conference.
The five-time Ballon d'Or victor fell awkwardly on his right arm in the 17th minute of the La Liga clash with Sevilla at the Camp Nou on Saturday and was immediately in visible pain.
Barca will hope the injury to their star player is not serious, particularly with a handful of hard fixtures coming up.
Local media immediately questioned whether Madrid should fire Lopetegui before the clasico next weekend at Barcelona or give him a chance to try to save his job against the rival.
On that day, Julio Baptista scored the only goal of the game to collect all three points for Bernd Schuster's side. Ousmane Dembele came on for Messi. Luis Suarez added the third by converting a second-half penalty kick.
Barcelona were able to see out the game against Sevilla with a 4-2 victory, but the atmosphere remained subdued due to the uncertainty over Messi.
The game seemed up but Marc-Andre ter Stegen had to make a brilliant double save to deny Sarabia and then Wissam Ben Yedder with his thigh.