The victory has soothed a turbulent week that saw the shock resignation of president Sandro Rosell and a whirlwind of allegations concerning Brazilian striker Neymar.
Gerard Pique opened the scoring just before the break and then Pedro Rodriguez and Alexis Sanchez notched twice in quick succession around the hour mark to complete the scoring.
It would have been an even bigger margin of victory for the reigning champions but they twice saw efforts came back off the post while Malaga goalkeeper Willy Caballero made a string of saves.
It was the perfect end to a testing few days for the Catalan giants.
Rosell's decision to relinquish the presidency on Thursday night came as he defends himself against allegations he misappropriated funds from the signing of striker Neymar last summer.
Real Madrid had also briefly taken top spot from them by beating Granada 2-0 on Saturday.
However, far from letting those incidents affect their performance against Malaga, Barca dominated from start to finish at the Nou Camp to reclaim top spot on goal difference from Atletico Madrid - who themselves had leap-frogged back above Realearlier on Sunday with a 4-2 win over Rayo Vallecano.
Barca, with new president Josep Maria Bartomeu watching on after he was named as Rosell's successor, came within inches of taking the lead after just five minutes when Alexis dinked the ball past Willy only to see it strike the far post.
Lionel Messi also failed to make the most of a similar opening as he lofted the ball wide with only Willy to beat before Pedro was denied by the visiting keeper.
Barca were dominating but they almost found themselves trailing in the 30th minute when Bartlomiej Pawlowski glanced a Sergio Duda header goalwards.
Fortunately for the home side though, it was straight at Victor Valdes and he was able to deflect it away.
That was a rare first-half scare for Barca and Pedro and Jordi Alba both went close before they broke the deadlock in the 40th minute.
Xavi's corner was flicked on by Alexis at the near post and the unmarked Pique had time to control the ball before drilling a half-volley past Willy.
Barca's dominance continued after the break with Willy superbly saving from Alexis and Cesc Fabregas before Pique saw his header come back off the post.
It seemed only a matter of time before Barca notched a second goal though, and it arrived in the 55th minute when Pedro created space inside the area before curling a low shot just inside the far post.
Malaga tried to pull a goal back with an audacious long-range effort by Duda, which was clawed away by Valdes, but it was game over in the 61st minute when Barca added a third.
Messi threaded the ball to Pedro whose first-time pass was slotted home at the far post by Alexis as Barca returned back to their perch atop the La Liga standings.