ill-advised back pass by Malaga's Ignacio Camacho to net for a ninth straight league game in the 27th minute. He then set up Cesc Fabregas to score in the 50th and substitute Thiago Alcantara to add another eight minutes from time.
Barcelona has won all 10 away games this season and is unbeaten in the league after a league-record start of 18 wins to go with one single draw.
The season is still far from over, but Barcelona looks set to recover its domestic crown. The Catalan club maintained its commanding 11-point lead over Atletico Madrid after its nearest chaser beat Real Zaragoza 2-0.
"We started the season very strong, winning almost all the points possible, and we have kept it up through the first half," said Barcelona forward Pedro Rodriguez. "We hope we can continue. We always have new goals to keep us motivated. We just have to go forward game by game."
While Atletico is theoretically still in the hunt, Barcelona's victory left defending champion Real Madrid in a distant third place 18 points adrift. That is the largest deficit Madrid has faced since it was 20 points behind league-leading Atletico in May 1996.
This game was billed as one of the toughest challenges Barcelona could face, and Malaga tried to press the visitors from the start.
But Malaga's challenge didn't last long. Barcelona's midfield trio of Andres Iniesta, Fabregas and Xavi Hernandez soon took control of the ball, while holding midfielder Sergio Busquets swept up everything in his path.
Messi then did the rest.
The Argentine's opener was a mixture of speed and stealth, as Camacho never saw Messi lurking as he sent the ball back toward his area. Messi raced in to scoop up the ball, cut back to bring goalkeeper Willy Caballero to the turf, and rolled the ball home.
Having scored a record 50 league goals last season, the Argentina star is on pace to surpass his own milestone. He already has a league-leading 28 goals so far this campaign.
Barcelona as a team is also on course to break Madrid's record point haul from last season when it finished with 100. Barcelona has 55 points at the season's halfway mark.
Messi created Barcelona's second goal just after halftime when he lobbed a perfect pass over defender Martin Demichelis for the streaking Fabregas to send off the far post and into the net with vicious right-footed stab.
Thiago then capped the win by dribbling past two defenders and linking up with Messi with a clever one-two passing combination before firing under Caballero.
Diego Buonanotte went off the bench to score from a free kick and give Malaga a consolation goal with two minutes to play.
Coach Tito Vilanova was on the touchline for Barcelona's latest dazzling performance after returning from a trip to New York, reportedly to seek further treatment after he recently had a tumor removed from his a saliva gland for the second time in two years.
Malaga's loss meant it slid into fifth place, relinquishing Spain's last Champions League spot to Real Betis after it beat visiting Levante 2-0 earlier.
Radamel Falcao scored to help Atletico brush off Zaragoza, as Diego Simeone's team kept its perfect home record through 10 league games this season.
Tiago Cardoso broke through for Atletico in the 31st, and Falcao doubled the lead by driving home a penalty kick seven minutes later after Arda Turan was brought down in the box by Ionut Sapunaru. It was the Colombia striker's 18th goal of the season, second only to Messi.
Also, 10-man Deportivo La Coruna earned a 1-1 draw at Real Sociedad that allowed it to crawl out of the cellar and push Osasuna to the bottom of the standings.