Barcelona moved to the top of La Liga with an impressive two-goal success over in-form Sevilla, but the victory came at a cost as Messi was forced off the field in the first period.
The Argentine is now almost certain to miss Wednesday's Champions League clash with Inter Milan, and will also be a huge doubt for El Clasico next weekend.
Barcelona took the lead in just the second minute of the match when Messi's clever pass found Philippe Coutinho and the Brazilian curled the ball into the top corner of the net.
Sevilla came close to levelling four minutes later when Guilherme Arana struck one towards the bottom corner, but his effort smashed against the post as Barcelona survived a dangerous moment.
Messi had one deflected wide in the period that followed as chances continued to arrive, and it was not a surprise that the Argentine doubled Barcelona's lead in the 12th minute.
Indeed, Messi isolated Sevilla centre-back Sergi Gomez in a dangerous position before shifting the ball to one side and finding the bottom corner with an excellent strike.
Messi was forced to spend more than five minutes receiving treatment on the side of the pitch in the first half, however, with the attacker needing his arm bandaged following an awkward fall.
It appeared that the South American would return having been strapped up, but the decision was made to replace the 31-year-old, with Ousmane Dembele entering the field.
Dembele had Barcelona's next chance when he raced onto a Luis Suarez pass before striking towards goal, but the Frenchman's effort dropped wide of the far post, before Nelson Semedo hit the side-netting four minutes later.
Sevilla had an opportunity to halve the deficit in the closing stages of the first period when Pablo Sarabia met a low cross from Jesus Navas, but his effort was just wide. Moments later, Barcelona should have had a third, but Ivan Rakitic chipped harmlessly into the arms of Tomas Vaclik.
Vaclik kept out a Coutinho effort in the 52nd minute after a low-key start to the second period, before Luis Suarez struck wide of the post from distance two minutes later.
Luis Suarez then fired wide of Vaclik's goal just before the hour mark, before Barcelona goalkeeper Marc-Andre ter Stegen made excellent saves to keep out Andre Silva and Franco Vazquez in quick succession.
Barcelona put the game beyond Sevilla in the 63rd minute, however, when Luis Suarez, who had been fouled by Vaclik inside the Sevilla box, converted from the penalty spot.
Wissam Ben Yedder struck wide of the Barcelona post in the period that followed as Sevilla looked for a route back into the match, but Barcelona were threatening a fourth, and Vaclik did well to keep out a low strike from Luis Suarez.
Sevilla did indeed have one back in the 79th minute when Sarabia's deflected effort found a route past Ter Stegen.
The visitors then had two wonderful chances to score a second in the 86th minute when Sarabia and Ben Yedder both found themselves free inside the Barcelona box, but Ter Stegen made two more excellent saves.
The hosts then went down the other end and scored a fourth, with Rakitic's super volley finding the back of the net to secure all three points.
Sevilla were not finished, however, and added a second in the first minute of additional time when substitute Luis Muriel picked out the far corner with a curling effort.
BARCELONA (4-3-3): Ter Stegen; Semedo, Pique, Lenglet, Alba; Busquets, Rakitic, Arthur (Roberto 67'); Coutinho, Suarez (Munir El-Haddadi 81'), Messi (Dembele 26')
SEVILLA (3-5-2): Vaclik; Carrico, Gomez, Kjaer (Mercado 55'); Navas, Banega, Vazquez (Mesa 69'), Sarabia, Arana; Ben Yedder, Silva (Muriel 78')