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.
And 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.
Despite Messi's absence, Barca boss Gerardo Martino once again started with Neymar on the bench as Cesc 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.
Fabregas saw a looping header easily held by Caballero before Pedro just failed to take a defence splitting pass from the former Arsenal captain in his stride.
Andres Iniesta then fired another effort 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.
The pattern continued after the interval as Barca continued to probe, without looking overly threatening.
Gerard Pique nearly added a fortunate second 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 per cent 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 Atletico ahead of the second-leg of the Super Cup at the Camp Nou on Wednesday.