The European champions were handed the perfect start when Munir El Haddadi tapped home the opener after just 64 seconds, but were far from their best and Malaga deservedly levelled through Juanpi either minutes before the break.
Messi had been struggling with a slight hamstring strain in the past week, but the five-time World Player of the Year made the difference once more as he volleyed home his 20th goal of the season to move Barca a point clear of Atletico Madrid in top spot.
Atletico and Real Madrid – who now trail Barca by five points – are both in action on Sunday when they face Sevilla and Real Betis respectively.
Barcelona were without the injured Neymar and suspended Gerard Pique, but did have the luxury of welcoming back Messi and Luis Suarez after they missed the 2-1 win Copa del Rey win at Athletic Bilbao in midweek.
And Suarez made a telling impact after just a minute as he wriggled clear inside the area and although his low shot was kept out by Carlos Kameni, the ball fell invitingly for El Haddadi to tap home his fourth goal in three games.