The Portugal international fired home a low strike after beating three Malaga defenders in the 23rd minute to claim a narrow victory for Real which put the pressure back on capital rivals Atletico Madrid who lie second in the overall standings.
The result left Malaga in 13th place but only three points clear of the relegation zone.
Ronaldo started off on the front foot and tested Malaga goalkeeper Willy Caballero with a strike from the edge of the area shortly after he forced a block from Marcos Angeleri.
Isco went close from a corner but Malaga also had an early chance when Roque Santa Cruz headed over from close range in the 13th minute.
However, it was Real who broke the deadlock midway through the first half when Ronaldo received a ball from Gareth Bale in the left of the box, cut back inside and curled it into the bottom of the net.
That proved to be the only goal of the game despite several chances for both sides, with Caballero making an excellent save with his feet to deny Ronaldo just over a minute after his score.
Malaga's Nordin Amrabat forced a save from Real keeper Diego Lopez just after the half hour mark before he fired over the bar 10 minutes later.
Isco flashed a shot over the bar early in the second half with Amrabat hardly testing Lopez at his next attempt, the keeper making a comfortable save.
Real defender Marcelo had a shot blocked by Sergio Sanchez in the 74th minute as both sides struggled to find a breakthrough with Ronaldo's next chance caught by Caballero.
Both sides kept plugging away for a goal as the clock ticked down but their search proved to be elusive.