The Argentinian star was withdrawn at half-time during the first leg of the Spanish Super Cup against Atletico Madrid on Wednesday with a thigh injury.
The club's medical staff will continue to assess the player before determining whether he will be fit to play at La Rosaleda on Sunday.
Barcelona will otherwise be in good spirits after opening their La Liga campaign with a stunning 7-0 demolition of Levante in new coach Gerardo Martino's first game last weekend.
Their big summer signing, £50million man Neymar, did not get on the scoresheet in that game but did strike to secure a 1-1 draw against Atletico in the Spanish capital in midweek.
Sunday's game will bring Barca up against a familiar face in Bernd Schuster.
The German spent four years as a player at the Nou Camp in the 1980s before controversially joining Real Madrid and then going on to coach Los Blancos.
Schuster, who has also coached Levante and Getafe, took charge at Malaga in the summer following Manuel Pellegrini's move to Manchester City.
They are yet to get their campaign up and running after losing 1-0 at Valencia but defender or winger Vitorino Antunes claims there can be no better motivation than a visit from Barca.
Antunes told reporters: "I've got a great respect for them, but then I do for every team.
"We know that Barcelona are one of the best teams in the world, so playing them is a great motivation for us.
"We want to win our first home game of the season, all the more being against Barcelona, and will be doing all we can to earn the three points.
"They are a fantastic team and present a difficult game for any rival.
"However it's 11 against 11 on the pitch and we're determined to win.
"If we give it our all on Sunday, we're capable of victory and playing very good football."
Antunes insists his team-mates will not get over-confident if Messi, Barca's record goalscorer, fails to make the contest.
He said: "Messi is such a strong player, and if he's not in Sunday's line-up then it's better for us.
"However Barcelona have other quality players, and the team doesn't just rely on Messi."