Diego Simeone's men came off second best during the first half at La Rosaleda but their 21-year-old midfielder secured three precious points with his 70th-minute strike
The Rojiblancos struggled to get going during the opening half at the Rosaleda but they improved after the interval and claimed a crucial victory when their homegrown 21-year-old midfielder fired home with just 20 minutes remaining.
With winter champion Barcelona hosting Elche on Sunday, Atletico went into the game knowing that it would almost certainly have to win at Malaga if it was to end the weekend still level on points with the Blaugrana at the summit of the standings.
However, it was Malaga which began the brighter of the two sides, with defender Sergio Sanchez firing over the bar seven minutes in, after the ball had dropped invitingly for him in the area.
Indeed, the Rojiblancos did not threaten the home side's goal until the 23rd minute, when Willy Caballero dealt easily with a low drive from Juanfran.
The hosts upped the ante just after the half-hour mark, with Eliseu Pereira testing Thibaut Courtois at the end of an incisive drive into the area.
Vitorino Antunes let fly just moments later but his curling effort from wide on the right-hand side never looked like creeping inside the far post.
Still, there was no denying that Malaga looked the more likely as a slightly underwhelming first half drew to a close.
Credit to Diego Simeone's men, though, they looked far more energetic after the break, with the introduction of Adrian Lopez in place of the ineffective Oliver Torres playing a key role in their transformation.
Indeed, Adrian went close to opening the scoring on 62 minutes after finding some space in the area but he was closed down by Antunes at the last second.
However, Atletico finally made the breakthrough soon after when Koke pounced on a loose ball and calmly fired home to secure three precious points for the visitors.