The Brazilian struck the decisive blow a minute before half-time with a left-footed effort that Malaga goalkeeper Willy Caballero will have been disappointed to see slip through his grasp.
However, Malaga were left to rue two huge chances after the break as firstly Fabrice struck the post and then Sebastian Fernandez headed straight at Victor Valdes when completely unmarked inside the area in the closing stages.
And Cesc Fabregas admitted that going forward the Catalans will need to improve on their performance in the second period.
“The first-half was very good and we could have scored more,” he told Canal Plus.
“In the second it is true that we lost a bit of our intensity due to tiredness from the game on Wednesday.
“In the last five minutes we struggled but sometimes you have to do that. It was a hard-fought and important victory.”
Despite Messi’s absence, Barca boss Gerardo Martino once again started with Neymar on the bench as Fabregas replaced the Argentine, whilst Alex Song and Adriano replaced Sergio Busquets and Dani Alves from the side that started Wednesday’s 1-1 draw with Atletico Madrid in the first-leg of the Spanish Super Cup.
Without either of their South American attacking stars, Barca’s build-up play was somewhat ponderous in the first period as they failed to break down a solid but limited Malaga side.
Andres Iniesta then fired an effort from the edge of the area straight down Caballero’s throat, but the Argentine was forced into a stunning save nine minutes before the break as he blocked Alexis Sanchez’s header from point-blank range.
However, Caballero was slightly at fault when Barca did eventually take the lead as Adriano cut inside onto his left foot and his curling effort flew over the Malaga keeper’s outstretched arm on its way into the far corner.
Gerard Pique nearly added a fortunate second after the break as Xavi’s free-kick rebounded off the defender’s back and looped off the crossbar before Martino finally introduced Neymar just after the hour mark.
Malaga then passed up a huge opportunity to level with their first clear opening of the match as Roque Santa Cruz rounded Valdes and from a tight angle cut the ball back for Fabrice, but the young Cameroonian could only pull his effort off the base of the post.
Neymar nearly made it two goals in as many games with a well-struck free-kick that Caballero did well to parry to safety.
And Malaga passed up another great chance in the final minute as Jesus Gamez’s cross found Fernandez completely unmarked, only for the Uruguayan to head straight at Valdes, while the Barca keeper comfortably held Fernando Tissone’s follow-up.
Barca’s win took them to the top the table by a single goal ahead of Atletico Madrid after Diego Simeone’s men continued their 100 percent record in the league with a 5-0 mauling of Rayo Vallecano at the Vicente Calderon.
Raul Garcia, Diego Costa and Arda Turan had the hosts 3-0 up after just 34 minutes and further goals from Tiago and Garcia after the break rounded off a perfect afternoon for Atleti ahead of the second-leg of the Super Cup at the Camp Nou on Wednesday.
Elsewhere, Sevilla’s faltering start to their league campaign continued as they could only manage a 0-0 draw away to Levante.
And it was an even worse night for the other half of Seville as Real Betis lost 2-1 at home to Celta Vigo.