The injury will ruled the Barca captain out of the clasico against arch rivals Real Madrid next week and up to five other games.
The Argentine was left writhing in agony after landing heavily on his right arm after colliding with Franco Vazquez.
"Psychologically we know that when he is there we are stronger but we can not allow his absence to affect us", Barca centre-back Pique said. Of course we're going to notice not having Messi, we know that.
Messi will miss playing Inter Milan in the Champions League on Wednesday, and El Clasico against Real Madrid next weekend.
Leo is fundamental, but that's what we will try: "to maintain the same idea and move forward", Pique said. "But it does not have to affect us".
The hosts picked up from where they left off in the first half, and managed to bag a third goal in the 63rd minute when Luis Suarez converted a penalty that he won.
Until Messi's injury, it had been an ideal start for Barca.
Barca fans had chanted, "don´t touch the badge" before kick-off after president Josep Maria Bartomeu had announced plans to change the club crest had been shelved.
However, Rakitic restored Barca's three-goal advantage with a superb volley that sailed into the bottom corner.
"He did enough didn´t he?"
He was replaced by Ousmane Dembele on Saturday.
Sarabia's 79th-minute reply took a vital deflection off former Sevilla defender Clement Lenglet to ruin Ter Stegen's clean sheet, the Germany goalkeeper then making a second double save.