Messi had to be substituted in the 26th minute at the Camp Nou after falling awkwardly on his right arm, but not before the Argentinian had doubled Barca’s lead with a curling left-footed finish.
Barcelona now face an anxious wait, with the Clasico against Real Madrid fast-approaching next weekend.
Philippe Coutinho had opened the scoring and Luis Suarez’s penalty, which he also earned, made sure of victory before a three-goal flurry in the final 11 minutes.
Pablo Sarabia and Luis Muriel twice reduced the deficit to two, either side of a sweeping volley from Ivan Rakitic.
Any joy at jumping above in-form Sevilla, however, was tarnished by the injury to Messi.
Before the clash against Madrid next Sunday, Inter Milan visit in the Champions League on Wednesday but Messi’s involvement there would seem unlikely.
He fell to the ground following a tussle with Sevilla’s Franco Vazquez and, as his right hand tried to cushion the landing, his elbow appeared to buckle.
Messi was helped off the pitch by medical staff and, despite having his right arm heavily strapped while Barca played for nine minutes with 10 men, he finally trudged off down the tunnel.
If the injury proves serious, the timing could hardly be worse, given Ernesto Valverde’s team face a difficult run of fixtures over the next month.
After Inter and Real, whose poor form continued with a loss at home to Levante earlier on Saturday, Barca’s schedule includes the return tie against Inter in Italy, as well as La Liga games against Real Betis and Atletico Madrid.
Even without Messi, they might be confident of seeing off Madrid, whose early-season dip has only deepened while Barcelona have sparked a rival.
Since drawing at home to Athletic Bilbao last month to make it three games without a win, they have blown Tottenham away at Wembley, taken a point away to Valencia and now eased past Sevilla, who came into the weekend top of the table.
Barca fans had chanted, “don’t touch the badge” before kick-off after president Josep Maria Bartomeu had announced earlier on Saturday that plans to change the club crest had been shelved.
They were soon celebrating a goal too as Coutinho bent a sumptuous right-footed shot into the far corner with only two minutes on the clock.
Messi doubled the advantage, racing clear on the counter-attack before jinking inside and curling into the bottom corner with his left foot. It was his last significant contribution.
Ousmane Dembele was his replacement but Suarez took on the mantle, too quick to his own heavy touch and brought down by Sevilla goalkeeper Tomas Vaclik. Suarez buried the penalty.
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.
Sarabia gave Sevilla hope with 11 minutes left, his shot deflecting off Clement Lenglet and in, but Rakitic ensured there was to be no late drama with a well-timed volley. Muriel added what proved only to be a consolation in injury time.